RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17766
(148 letters)
>gnl|CDD|197718 smart00427, H2B, Histone H2B.
Length = 97
Score = 119 bits (300), Expect = 5e-36
Identities = 58/70 (82%), Positives = 67/70 (95%)
Query: 77 INIKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSE 136
I+ +AMSIMNSFVNDIFERIAAE+S+LA YNK+ST++SREIQTAVRL+LPGELAKHAVSE
Sbjct: 28 ISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSE 87
Query: 137 GTKAVTKYTS 146
GTKAVTK +S
Sbjct: 88 GTKAVTKASS 97
Score = 115 bits (290), Expect = 1e-34
Identities = 56/65 (86%), Positives = 63/65 (96%)
Query: 1 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 60
MSIMNSFVNDIFERIAAE+S+LA YNK+ST++SREIQTAVRL+LPGELAKHAVSEGTKAV
Sbjct: 33 MSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEGTKAV 92
Query: 61 TKYTS 65
TK +S
Sbjct: 93 TKASS 97
>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional.
Length = 116
Score = 112 bits (281), Expect = 6e-33
Identities = 56/71 (78%), Positives = 66/71 (92%)
Query: 77 INIKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSE 136
I+ KAMSIMNSF+NDIFE+IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSE
Sbjct: 46 ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSE 105
Query: 137 GTKAVTKYTSS 147
GTKAVTK+TS+
Sbjct: 106 GTKAVTKFTSA 116
Score = 108 bits (271), Expect = 2e-31
Identities = 53/66 (80%), Positives = 62/66 (93%)
Query: 1 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 60
MSIMNSF+NDIFE+IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAV
Sbjct: 51 MSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAV 110
Query: 61 TKYTSS 66
TK+TS+
Sbjct: 111 TKFTSA 116
>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional.
Length = 117
Score = 92.2 bits (228), Expect = 5e-25
Identities = 50/70 (71%), Positives = 62/70 (88%)
Query: 77 INIKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSE 136
I+ K+M+IMNSF+ D FE+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSE
Sbjct: 47 ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSE 106
Query: 137 GTKAVTKYTS 146
GTKAVTK+TS
Sbjct: 107 GTKAVTKFTS 116
Score = 89.5 bits (221), Expect = 5e-24
Identities = 48/65 (73%), Positives = 58/65 (89%)
Query: 1 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 60
M+IMNSF+ D FE+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAV
Sbjct: 52 MNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAV 111
Query: 61 TKYTS 65
TK+TS
Sbjct: 112 TKFTS 116
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 63.0 bits (154), Expect = 3e-14
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 77 INIKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 124
I+ KA + + D+ E I ++ LA + KR TIT R+IQ AVRL
Sbjct: 28 ISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAVRLD 75
Score = 59.5 bits (145), Expect = 8e-13
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 1 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 43
+ + D+ E I ++ LA + KR TIT R+IQ AVRL
Sbjct: 33 PVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAVRLD 75
>gnl|CDD|238665 cd01369, KISc_KHC_KIF5, Kinesin motor domain, kinesin heavy chain
(KHC) or KIF5-like subgroup. Members of this group have
been associated with organelle transport. This catalytic
(head) domain has ATPase activity and belongs to the
larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 325
Score = 28.0 bits (63), Expect = 2.1
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 64 TSSNDTLSVLVLPINIKAMSIMNSFVNDIFERIAAESSRLAHYNKRS 110
T S T ++ P + + I+ V+DIFE I++ L + K S
Sbjct: 86 TGSGKTYTMEGPPGDPELKGIIPRIVHDIFEHISSMDENLEFHVKVS 132
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 25.8 bits (57), Expect = 4.5
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 80 KAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 127
A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 40 SAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
Score = 25.4 bits (56), Expect = 6.4
Identities = 11/43 (25%), Positives = 23/43 (53%)
Query: 4 MNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 46
+ + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 45 LQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>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 = 25.8 bits (57), Expect = 6.2
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 11 IFERIAAESSRLA----HYNKRSTITSREIQTAVR 41
+ E + AE LA NK+ IT R +Q AVR
Sbjct: 50 VLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84
Score = 25.8 bits (57), Expect = 6.2
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 92 IFERIAAESSRLA----HYNKRSTITSREIQTAVR 122
+ E + AE LA NK+ IT R +Q AVR
Sbjct: 50 VLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84
>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 = 24.9 bits (55), Expect = 6.9
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 3 IMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 37
I + FV+D+ E + RLA + K T+ +++Q
Sbjct: 31 IADDFVDDVVED----ACRLAKHRKSDTLEVKDVQ 61
Score = 24.9 bits (55), Expect = 6.9
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 84 IMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 118
I + FV+D+ E + RLA + K T+ +++Q
Sbjct: 31 IADDFVDDVVED----ACRLAKHRKSDTLEVKDVQ 61
>gnl|CDD|217710 pfam03747, ADP_ribosyl_GH, ADP-ribosylglycohydrolase. This family
includes enzymes that ADP-ribosylations, for example
ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves
ADP-ribose-L-arginine. The family also includes
dinitrogenase reductase activating glycohydrolase. Most
surprisingly the family also includes jellyfish
crystallins, these proteins appear to have lost the
presumed active site residues.
Length = 284
Score = 26.2 bits (58), Expect = 7.6
Identities = 12/60 (20%), Positives = 25/60 (41%)
Query: 10 DIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSNDT 69
+ +A E +RL H + R+ + + AV L L G+ A+ + + ++
Sbjct: 138 EEAAELAREDARLTHGHPRAVAGAVAVAAAVALALRGKDLDEALDAALALLGLIPADSEL 197
Score = 26.2 bits (58), Expect = 7.8
Identities = 12/57 (21%), Positives = 23/57 (40%)
Query: 91 DIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 147
+ +A E +RL H + R+ + + AV L L G+ A+ + +
Sbjct: 138 EEAAELAREDARLTHGHPRAVAGAVAVAAAVALALRGKDLDEALDAALALLGLIPAD 194
>gnl|CDD|216687 pfam01763, Herpes_UL6, Herpesvirus UL6 like. This family consists
of various proteins from the herpesviridae that are
similar to herpes simplex virus type I UL6 virion
protein. UL6 is essential for cleavage and packaging of
the viral genome.
Length = 556
Score = 26.0 bits (58), Expect = 8.8
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 66 SNDTLSVLVLP-----INIKAM-SIMNSFVNDIFERIAA---ESSRLAHY 106
SNDT+S+L+ P + + + I ++ E + + SRL Y
Sbjct: 498 SNDTISLLLGPFFYSVLKLPRLGLITEEYLYLSEEELCDALYKKSRLEVY 547
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 25.5 bits (56), Expect = 8.9
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 11 IFERIAAESSRLA----HYNKRSTITSREIQTAVR 41
+ E + AE LA NK+ IT R IQ A+R
Sbjct: 57 VLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91
Score = 25.5 bits (56), Expect = 8.9
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 92 IFERIAAESSRLA----HYNKRSTITSREIQTAVR 122
+ E + AE LA NK+ IT R IQ A+R
Sbjct: 57 VLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91
>gnl|CDD|165288 PHA02985, PHA02985, hypothetical protein; Provisional.
Length = 271
Score = 25.8 bits (57), Expect = 9.5
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 61 TKYTSSN---DTLSVLVLPINIKAMSIMNSFVNDI 92
+KYT S +L ++VL I+I +M I+ S +N+I
Sbjct: 121 SKYTVSKVSKGSLIIIVLDIDIPSMRIVYSSINNI 155
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 0.125 0.321
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: 6,846,497
Number of extensions: 579616
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 657
Number of HSP's successfully gapped: 39
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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: 41 (21.6 bits)
S2: 54 (24.8 bits)