RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17765
(475 letters)
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 204 bits (521), Expect = 1e-64
Identities = 87/117 (74%), Positives = 97/117 (82%), Gaps = 3/117 (2%)
Query: 121 TSSKGKGGKAKTKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEY 177
KGK G K K +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAV+EY
Sbjct: 1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60
Query: 178 LAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
L AEVLELAGNAA+DNKK RI PRH+QLAIRNDEELNKLL+GVTIA GGVLPNI V
Sbjct: 61 LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKV 117
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 200 bits (510), Expect = 3e-63
Identities = 90/109 (82%), Positives = 97/109 (88%)
Query: 127 GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 186
GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAV+EYL AEVLELA
Sbjct: 3 GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62
Query: 187 GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVR 235
GNAARDNKK RI PRHLQLA+RNDEELNKLL GVTIA GGVLPNI V
Sbjct: 63 GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKVL 111
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 195 bits (497), Expect = 5e-61
Identities = 85/111 (76%), Positives = 97/111 (87%)
Query: 124 KGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVL 183
K KGG K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAV+EYLAAEVL
Sbjct: 6 KRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVL 65
Query: 184 ELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
ELAGNAARDNKK+RI+PRH+QLA+RNDEEL+KLL GVTIA GGVLPNI +V
Sbjct: 66 ELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSV 116
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 192 bits (491), Expect = 1e-60
Identities = 88/99 (88%), Positives = 92/99 (92%)
Query: 136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 195
+RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAV+EYL AEVLELAGNAARDNKK
Sbjct: 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60
Query: 196 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
RI PRHLQLAIRNDEELNKLL GVTIAQGGVLPNI V
Sbjct: 61 RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKV 99
>gnl|CDD|197718 smart00427, H2B, Histone H2B.
Length = 97
Score = 175 bits (446), Expect = 5e-54
Identities = 81/97 (83%), Positives = 93/97 (95%)
Query: 26 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 86 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61 STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97
Score = 112 bits (282), Expect = 4e-30
Identities = 51/64 (79%), Positives = 61/64 (95%)
Query: 380 KKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 439
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 440 STIT 443
ST++
Sbjct: 61 STLS 64
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 176 bits (448), Expect = 9e-54
Identities = 87/119 (73%), Positives = 97/119 (81%), Gaps = 3/119 (2%)
Query: 119 KYTSSKGKGGKAK---TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVM 175
S KGG+ K TKS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AV+
Sbjct: 1 GAGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60
Query: 176 EYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
EYLAAEVLELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL VTIA GGVLPNI
Sbjct: 61 EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQT 119
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 166 bits (421), Expect = 8e-50
Identities = 89/113 (78%), Positives = 98/113 (86%), Gaps = 2/113 (1%)
Query: 123 SKGKGGKA--KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
S GKGGKA S++RS++AGL FPVGR+ RLL+KGNY R+GAGAPVYLAAV+EYLAA
Sbjct: 3 SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62
Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 233
E+LELAGNAARDNKK RIIPRHLQLAIRNDEELNKLL VTIAQGGVLPNI
Sbjct: 63 EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINP 115
>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional.
Length = 116
Score = 163 bits (413), Expect = 5e-49
Identities = 78/107 (72%), Positives = 92/107 (85%)
Query: 17 AQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAES 76
A+K + KK + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+IA E+
Sbjct: 10 AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEA 69
Query: 77 SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123
+LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 70 GKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Score = 103 bits (258), Expect = 1e-26
Identities = 47/73 (64%), Positives = 58/73 (79%)
Query: 371 AQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAES 430
A+K + KK + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+IA E+
Sbjct: 10 AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEA 69
Query: 431 SRLAHYNKRSTIT 443
+LA YNK+ T+T
Sbjct: 70 GKLARYNKKPTVT 82
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 162 bits (410), Expect = 2e-48
Identities = 86/119 (72%), Positives = 101/119 (84%)
Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
+ +GKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL AE
Sbjct: 2 AGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAE 61
Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
VLELAGNAARDNKK RI+PRH+QLAIRNDEEL KLL VTIA GGVLPNI AV + ++T
Sbjct: 62 VLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKT 120
>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional.
Length = 117
Score = 137 bits (347), Expect = 2e-39
Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)
Query: 12 KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 69
KK KA+K D KK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 70 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
E+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64 EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Score = 86.4 bits (213), Expect = 2e-20
Identities = 46/80 (57%), Positives = 60/80 (75%), Gaps = 2/80 (2%)
Query: 366 KKAGKAQKNITKSD--KKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 423
KK KA+K T D KK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 424 ERIAAESSRLAHYNKRSTIT 443
E+IA E+SRL Y +R T++
Sbjct: 64 EKIATEASRLCKYTRRDTLS 83
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 132 bits (334), Expect = 4e-37
Identities = 73/116 (62%), Positives = 86/116 (74%), Gaps = 2/116 (1%)
Query: 118 TKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVME 176
K T++ K K K K +RSSRAGLQFPVGRIHR L++ A RVGA A VY AA++E
Sbjct: 12 AKTTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILE 71
Query: 177 YLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 232
YL AEVLELAGNA++D K RI PRHLQLAIR DEEL+ L+ G TIA GGV+P+I
Sbjct: 72 YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIH 126
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 104 bits (260), Expect = 1e-26
Identities = 53/105 (50%), Positives = 74/105 (70%), Gaps = 2/105 (1%)
Query: 129 KAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN 188
KA RS++AGL FPVGR+ LLR+G YA R+GA VY+AAV+EYL AE+LEL+
Sbjct: 10 KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69
Query: 189 AARDN--KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNI 231
AA K R+ PR + LA+R+D++L LL VT+++GGV+P++
Sbjct: 70 AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSL 114
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 91.5 bits (228), Expect = 8e-23
Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 137 RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 195
S L+ P R+ R L++G YAE R+ + APV L +E L E+LE AG AR K+
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 196 TRIIPRHLQLAIRND 210
I PR +QLA+R D
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 89.2 bits (222), Expect = 5e-22
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 30 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85
R + +V++++ +SSKA + + D+ E I ++ LA + KR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 86 STITSREIQTAVRLL 100
TIT R+IQ AVRL
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 74.5 bits (184), Expect = 7e-17
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 386 RKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRST 441
R + +V++++ +SSKA + + D+ E I ++ LA + KR T
Sbjct: 3 RLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKT 62
Query: 442 IT-KDLCPSVCL 452
IT +D+ +V L
Sbjct: 63 ITPRDIQLAVRL 74
>gnl|CDD|165723 PLN00155, PLN00155, histone H2A; Provisional.
Length = 58
Score = 75.1 bits (184), Expect = 3e-17
Identities = 38/57 (66%), Positives = 48/57 (84%)
Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 178
+ +GKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL
Sbjct: 2 AGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 42.6 bits (100), Expect = 3e-05
Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%)
Query: 131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAA 190
+ K KTR FP+ R+ ++++ +VG PV + +E E++ L+ A
Sbjct: 17 QKKKKTR-------FPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEA 69
Query: 191 RDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQG 225
R R+ L+ A +DE+ + L +
Sbjct: 70 RKKSSKRMTSEFLKRATESDEKFDFLKNMEQFKNR 104
>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 = 34.9 bits (81), Expect = 0.006
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 204
P+ R+ R+++ A R+ A +A +E + A + K+ I H++
Sbjct: 3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62
Query: 205 LAI 207
LA+
Sbjct: 63 LAV 65
Score = 30.7 bits (70), Expect = 0.23
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 40 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 97
+ +++K +S A ++ V + E IA+E++ + KR TI + I+ AV
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
Score = 28.0 bits (63), Expect = 2.0
Identities = 12/52 (23%), Positives = 25/52 (48%)
Query: 394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKD 445
+ +++K +S A ++ V + E IA+E++ + KR TI +
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 30.8 bits (70), Expect = 0.32
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 53 VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 103
VSS A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>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 = 31.6 bits (72), Expect = 1.0
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 404 DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCV 463
GV + A+S + S+ N E AE R + +++ ++ P + YER
Sbjct: 150 AAGVEAIAVSSLFSYRNPEHELRVAEIIREIGPDIPVSLSHEVSPEI-----GEYERANT 204
Query: 464 TL 465
+
Sbjct: 205 AV 206
>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 = 31.2 bits (71), Expect = 1.4
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 5 KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIY----IYKVLKQVHPDTGVSSKAMSI 60
++ +V K+I + + + +E + + L + D S K ++
Sbjct: 98 EAKATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNL 157
Query: 61 M---NSFVNDIFERIAAESSRLAHYNKR 85
S + E + S +LA
Sbjct: 158 KDDLESLIASAKEELDQLSKKLAELKAE 185
Score = 30.8 bits (70), Expect = 1.6
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 359 KSSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIY----IYKVLKQVHPDTGVSSKAMSI 414
++ +V K+I + + + +E + + L + D S K ++
Sbjct: 98 EAKATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNL 157
Query: 415 M---NSFVNDIFERIAAESSRLAHYNKR 439
S + E + S +LA
Sbjct: 158 KDDLESLIASAKEELDQLSKKLAELKAE 185
>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 = 3.7
Identities = 10/51 (19%), Positives = 25/51 (49%)
Query: 44 LKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 94
LK++ P + ++ +D + + ++ RLA + K T+ +++Q
Sbjct: 11 LKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQ 61
>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID
subunit A.
Length = 67
Score = 26.9 bits (60), Expect = 4.6
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 40 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 94
+ +++Q+ +T + ++ +D E + + +LA + K + R+IQ
Sbjct: 5 LQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQ 59
>gnl|CDD|238717 cd01437, parp_like, Poly(ADP-ribose) polymerase (parp) catalytic
domain catalyses the covalent attachment of ADP-ribose
units from NAD+ to itself and to a limited number of
other DNA binding proteins, which decreases their
affinity for DNA. Poly(ADP-ribose) polymerase is a
regulatory component induced by DNA damage. The
carboxyl-terminal region is the most highly conserved
region of the protein. Experiments have shown that a
carboxyl 40 kDa fragment is still catalytically active.
Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP,
tankyrase) catalyze the addition of up to 100 ADP_ribose
units from NAD+. PARPs 1 and 2 are localized in the
nucleaus, bind DNA, and are activated by DNA damage.
VPARP is part of the vault ribonucleoprotein complex.
Tankyrases regulates telomere length through
interactions with telomere repeat binding factor 1.
Length = 347
Score = 29.2 bits (66), Expect = 5.0
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 97 VRLLLPGELA-------KHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGR 149
LLL E+A K A + S KG G A S+ G+ P+G+
Sbjct: 254 TGLLLLCEVALGKMNELKKADYMAKELPKGKHSVKGLGKTAPDPSEFEIDLDGVVVPLGK 313
Query: 150 I 150
Sbjct: 314 P 314
>gnl|CDD|237406 PRK13515, PRK13515, carboxylate-amine ligase; Provisional.
Length = 371
Score = 28.8 bits (65), Expect = 6.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 147 VGRIHRLLRKGNYAER---VGAGAPVYLAAVMEYLAAEVLE 184
V +L +G A+R V A L AV+++L E LE
Sbjct: 326 VEYARTILEEGTSADRQLRVYAETGGALRAVVDWLIEETLE 366
>gnl|CDD|215884 pfam00375, SDF, Sodium:dicarboxylate symporter family.
Length = 388
Score = 28.6 bits (65), Expect = 6.6
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 2/68 (2%)
Query: 302 SGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSES--LSSLTTADLLSITMAAGK 359
G L + S + LD + P + A+ +E L + A L I +AA
Sbjct: 95 VGLLLSAASAESAKTLEVPSLLDFLLNIIPSNIFAALAEGNVLQVIVFAILFGIALAALG 154
Query: 360 SSGKAVKK 367
GK + K
Sbjct: 155 EKGKPLLK 162
>gnl|CDD|220258 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
(CRISPR_cse1). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry, represented by
CT1972 from Chlorobaculum tepidum, is found in the
CRISPR/Cas subtype Ecoli regions of many bacteria (most
of which are mesophiles), and not in Archaea. It is
designated Cse1.
Length = 475
Score = 28.9 bits (65), Expect = 6.9
Identities = 15/99 (15%), Positives = 30/99 (30%), Gaps = 8/99 (8%)
Query: 315 TDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAGKSSGKAVKKAGKAQKN 374
D + + P+P E L + + + A ++ A+K+A A
Sbjct: 356 MDNMQAKWYEWRMDLLPLPAALLSDEDLRA-QIKEAVDAAEEAARALRSALKEAWFALGK 414
Query: 375 ITKSDKKKKPRRKESYAIY-------IYKVLKQVHPDTG 406
K DK + + ++L + D
Sbjct: 415 DAKGDKSFVDLAGRAEERFWQRLESAFRRLLADLEEDDD 453
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 28.6 bits (64), Expect = 7.9
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 334 LGASFSESLSSLTTADLLSITMAAGKSSGKAVKKAGKAQKNITKSDKKKKPRR 386
S ++ + A + +I AG S K K K ++++TK K KP
Sbjct: 216 AAESLEAAIENRDLATVKAIINLAGASRAKKFGK--KPKRSVTKRAKPAKPVA 266
>gnl|CDD|233961 TIGR02644, Y_phosphoryl, pyrimidine-nucleoside phosphorylase. In
general, members of this protein family are designated
pyrimidine-nucleoside phosphorylase, enzyme family EC
2.4.2.2, as in Bacillus subtilis, and more narrowly as
the enzyme family EC 2.4.2.4, thymidine phosphorylase
(alternate name: pyrimidine phosphorylase), as in
Escherichia coli. The set of proteins encompassed by
this model is designated subfamily rather than equivalog
for this reason; the protein name from this model should
be used when TIGR02643 does not score above trusted
cutoff [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 405
Score = 28.4 bits (64), Expect = 8.5
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 16/116 (13%)
Query: 166 GAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQG 225
P L + LAAE+L LAG A+ K+ R + + + + L K V AQG
Sbjct: 261 EGPADLKELTLALAAEMLLLAG-IAKTEKEAR---ALAEDVLESGKALEKFRRFVE-AQG 315
Query: 226 GVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDG 281
G I+ L L + + ++A++ + D LG+ V G
Sbjct: 316 GDPDVIKN-----------LDKLPKAKYKEEVKAEKSGYISEIDAEELGLAAVDLG 360
>gnl|CDD|148326 pfam06656, Tenui_PVC2, Tenuivirus PVC2 protein. This family
consists of several Tenuivirus PVC2 proteins from Rice
grassy stunt virus, Maize stripe virus and Rice hoja
blanca virus. The function of this family is unknown.
Length = 785
Score = 28.6 bits (64), Expect = 8.9
Identities = 24/101 (23%), Positives = 42/101 (41%), Gaps = 16/101 (15%)
Query: 289 EHLENATGLLVDE--SGNTLDSTSTR-----QTTDGGLG-DSLDVVTEYFPVPLGASFSE 340
E +E+ + +E N L T + ++GG+ D++DV PV L E
Sbjct: 575 EAIEDTPNIRYEENDGINMLTDTLSEPLKGVVVSEGGISLDTMDV----LPVTLSIKSKE 630
Query: 341 SLSSLTTADLLSITMAAGKSSGKAV-KKAGKAQKNITKSDK 380
++S+ T+ I++ K K V +K K + K
Sbjct: 631 KITSIITSR---ISLNNTKCKIKGVERKFKKTIIKVYTPSK 668
>gnl|CDD|233866 TIGR02435, CobG, precorrin-3B synthase. An iron-sulfur protein. An
oxygen atom from dioxygen is incorporated into the
macrocycle at C-20. In the aerobic cobalamin biosythesis
pathway, four enzymes are involved in the conversion of
precorrin-3A to precorrin-6A. The first of the four
steps is carried out by EC 1.14.13.83, precorrin-3B
synthase (CobG), yielding precorrin-3B as the product.
This is followed by three methylation reactions, which
introduce a methyl group at C-17 (CobJ; EC 2.1.1.131),
C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152)
of the macrocycle, giving rise to precorrin-4,
precorrin-5 and precorrin-6A, respectively [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 390
Score = 28.2 bits (63), Expect = 9.6
Identities = 32/117 (27%), Positives = 46/117 (39%), Gaps = 13/117 (11%)
Query: 138 SSRAGLQF-PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKT 196
++R LQ + H L + A +GA A + EV LAG + T
Sbjct: 52 TARGNLQLRGLTADHDALSQALLAAGLGAAGA----AADDIRNIEVSPLAGIDPGEIADT 107
Query: 197 RIIPRHLQLAIRNDEELNKLLS--GVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQG 251
R + L+ A+ N+ L +L V I GG L +L T V L +L G
Sbjct: 108 RPLAAELRAALENERALLELPPKFSVAIDGGGRLV------LLGDTADVRLQALTTG 158
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
0.314 0.129 0.354
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: 23,241,387
Number of extensions: 2260323
Number of successful extensions: 1897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1883
Number of HSP's successfully gapped: 59
Length of query: 475
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 374
Effective length of database: 6,457,848
Effective search space: 2415235152
Effective search space used: 2415235152
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 (22.0 bits)
S2: 61 (27.5 bits)