RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10959
(132 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 225 bits (574), Expect = 1e-77
Identities = 124/136 (91%), Positives = 130/136 (95%), Gaps = 4/136 (2%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTE 56
MARTKQTARKSTGGKAPRKQLA+KAARKSAP TGG+KKPHR TVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTE 60
Query: 57 LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI 116
LLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 117 MPKDIQLARRIRGERA 132
MPKDIQLARRIRGER+
Sbjct: 121 MPKDIQLARRIRGERS 136
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 199 bits (507), Expect = 2e-67
Identities = 126/136 (92%), Positives = 131/136 (96%), Gaps = 4/136 (2%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTE 56
MARTKQTARKSTGGKAPRKQLATKAARKSAP+TGGVKKPHR TVALREIR+YQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTE 60
Query: 57 LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI 116
LLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 117 MPKDIQLARRIRGERA 132
MPKDIQLARRIRGERA
Sbjct: 121 MPKDIQLARRIRGERA 136
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 156 bits (395), Expect = 1e-50
Identities = 84/105 (80%), Positives = 88/105 (83%), Gaps = 6/105 (5%)
Query: 34 GGVKKPHR----TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSAAIG 87
GG K R VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQS+AI
Sbjct: 1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIM 60
Query: 88 ALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 132
ALQEA+EAYLVGLFEDTNL AIHAKRVTIMPKDIQLARRIRGER
Sbjct: 61 ALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGERL 105
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 122 bits (308), Expect = 4e-37
Identities = 79/134 (58%), Positives = 96/134 (71%), Gaps = 12/134 (8%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTE 56
MAR Q ++ GK P+K+ + ++ KKPHR TVALREIR+YQKSTE
Sbjct: 1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTE 53
Query: 57 LLIRKLPFQRLVREIAQDFKTD-LRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVT 115
LLIRKLPF RLVREI+ + + R+ + A+ ALQEA+E +LV LFED NLCAIHAKRVT
Sbjct: 54 LLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVT 113
Query: 116 IMPKDIQLARRIRG 129
IMPKD+QLARRIRG
Sbjct: 114 IMPKDMQLARRIRG 127
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 112 bits (282), Expect = 1e-33
Identities = 63/88 (71%), Positives = 76/88 (86%), Gaps = 1/88 (1%)
Query: 44 ALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFE 102
AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q +AI ALQEA+EA+LVGLFE
Sbjct: 7 ALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFE 66
Query: 103 DTNLCAIHAKRVTIMPKDIQLARRIRGE 130
D+NLCAIH KRVTIMPKD+QLARRIRG+
Sbjct: 67 DSNLCAIHGKRVTIMPKDMQLARRIRGQ 94
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 103 bits (258), Expect = 5e-30
Identities = 41/75 (54%), Positives = 49/75 (65%)
Query: 54 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR 113
S+ LLI KLPF R+VRE+ + F +LR S A ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 114 VTIMPKDIQLARRIR 128
TI P+DIQLA R+
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 95.5 bits (238), Expect = 6e-27
Identities = 41/90 (45%), Positives = 56/90 (62%), Gaps = 5/90 (5%)
Query: 42 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLF 101
V L+EIRRYQ+ST+LL+ K P +R++R+ + R S+AI LQEA E YL +
Sbjct: 3 AVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEEIA 57
Query: 102 EDTNLCAIHAKRVTIMPKDIQLARRIRGER 131
ED A HAKR T+ +DI+LA + G R
Sbjct: 58 EDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 30.0 bits (67), Expect = 0.36
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 5 KQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR 41
K A+K KAP K++A K A K A K R
Sbjct: 1014 KAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGR 1050
Score = 26.9 bits (59), Expect = 4.1
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 2 ARTKQTARKSTGGKAP------RKQLATKAARKSAPSTGGVKKPHRTVALRE 47
A K+ A+K+ KA +K A K K AP+ +KP A ++
Sbjct: 991 AMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKK 1042
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 29.4 bits (66), Expect = 0.52
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 11 STGGKAPRKQLATKAARKSAPSTGGVKKPHRTVALREIRRYQKSTELLIRKL 62
KAPR+QL K R KK +V +R+ +K I +
Sbjct: 467 FGNVKAPRQQLNIK--RPEESEESEGKKQSSSVGIRDKSGTKKDILSAIENV 516
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.1 bits (63), Expect = 0.53
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 55 TELLIRKLPFQRLVREIAQDFKT 77
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>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 = 28.8 bits (65), Expect = 0.83
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 18/62 (29%)
Query: 68 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127
+ +A+D + LR I +QEA++ H+KR + D+ A R+
Sbjct: 22 AQLLAEDVEYRLR----EI--IQEAAK------------FMRHSKRRKLTTSDVNHALRL 63
Query: 128 RG 129
R
Sbjct: 64 RN 65
>gnl|CDD|202084 pfam01997, Translin, Translin family. Members of this family
include Translin that interacts with DNA and forms a
ring around the DNA. This family also includes human
translin-associated protein X, which was found to
interact with translin with yeast two-hybrid screen.
Length = 187
Score = 28.3 bits (64), Expect = 0.97
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 46 REIRRYQKSTELLIRKLPF----------QRLVREIAQDFKT--DLRFQSAAIGALQEAS 93
R+I R K + + + L+ ++ + K R+ A ALQE
Sbjct: 12 RDITRLSKKAIFALHRGDAEEAEELLKEAKELLAKLKELLKGHPYYRYSGAWSNALQEYV 71
Query: 94 EAYL 97
EA
Sbjct: 72 EALT 75
>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 = 1.4
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 58 LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIM 117
++ K Q L++EI + L E ++ ++ + ED A H K T+
Sbjct: 1 ILTKRKLQELLKEIDPR----EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLE 56
Query: 118 PKDIQLA 124
KD+QL
Sbjct: 57 VKDVQLH 63
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 28.2 bits (64), Expect = 1.5
Identities = 22/95 (23%), Positives = 29/95 (30%), Gaps = 19/95 (20%)
Query: 50 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEA--------------SEA 95
R++ L R L V Q D A L + SEA
Sbjct: 569 RWEAGQRLATRLL--LANVARHGQPLSLDEALIDAFRAVLLDESLDPAFAAELLTLPSEA 626
Query: 96 YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130
L E + AIHA R + LA ++ E
Sbjct: 627 ELAEQMEVIDPDAIHAAREALR---RALATALKDE 658
>gnl|CDD|173963 cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9
(TAF9) 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 9 (TAF9) is one of several TAFs that bind TBP and
are involved in forming the 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. 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 TAFs orthologs and paralogs. Human TAF9 has a
paralogue gene (TAF9L) which has a redundant function.
Several hypotheses are proposed for TAF function such as
serving as activator-binding sites, in core-promoter
recognition or a role in essential catalytic activity.
It has been shown that TAF9 interacts directly with
different transcription factors such as p53, herpes
simplex virus activator vp16 and the basal transcription
factor TFIIB. Each TAF, with the help of a specific
activator, is required only for expression of 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.
TAF9 is a component of TFIID in multiple organisms as
well as different TBP-free TAF complexes containing the
GCN5-type histone acetyltransferase. Several TAFs
interact via histone-fold (HFD) motifs; 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. TFIID has a histone
octamer-like substructure. TAF9 is a shared subunit of
both, histone acetyltransferase complex (SAGA) and TFIID
complexes. TAF9 domain interacts with TAF6 to form a
novel histone-like heterodimer that is structurally
related to the histone H3 and H4 oligomer.
Length = 117
Score = 26.0 bits (58), Expect = 3.6
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 95 AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129
Y + +D + + HA + I D++LA + R
Sbjct: 33 RYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV 67
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 26.8 bits (59), Expect = 4.7
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVK 37
K A+K A K A +K+AP G+K
Sbjct: 882 PAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLK 917
>gnl|CDD|225055 COG2144, COG2144, Selenophosphate synthetase-related proteins
[General function prediction only].
Length = 324
Score = 26.6 bits (59), Expect = 4.8
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 45 LREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 78
L ++ + E ++RK P + VRE +F
Sbjct: 3 LEDLISELRLFEGILRKNPIKDAVREFLDEFYGA 36
>gnl|CDD|237549 PRK13897, PRK13897, type IV secretion system component VirD4;
Provisional.
Length = 606
Score = 26.3 bits (58), Expect = 5.5
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 51 YQKSTELLIRKLP 63
YQ++TE L RKLP
Sbjct: 388 YQQATEFLCRKLP 400
>gnl|CDD|132031 TIGR02986, restrict_Alw26I, type II restriction endonuclease,
Alw26I/Eco31I/Esp3I family. Members of this family are
type II restriction endonucleases of the
Alw26I/Eco31I/Esp3I family. Characterized specificities
of three members are GGTCTC, CGTCTC, and the shared
subsequence GTCTC [DNA metabolism,
Restriction/modification].
Length = 424
Score = 26.3 bits (58), Expect = 5.7
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 17/87 (19%)
Query: 49 RRYQKSTELLIRKLP--FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNL 106
+R +R + R++ I + F + + + A Y FE ++
Sbjct: 332 KRLSNI----LRSNQDTYMRILWYILSN--GGAEFLATLLK-PEYAEYNYT---FEGLDI 381
Query: 107 CAIHAKRVTIMPK-----DIQLARRIR 128
+ + V+ P+ D + ARR+R
Sbjct: 382 GTLFGEIVSKTPRNTKRADSEAARRVR 408
>gnl|CDD|240373 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 365
Score = 26.1 bits (58), Expect = 6.1
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 35 GVKKPHRTVALREIRRYQKSTELLIRKLPFQRL---VREI--AQDFKTDLRFQSAAIGAL 89
G+K P VA+ +++ + +LLI +P Q L + +I + K R S G +
Sbjct: 74 GIKLPDNIVAVSDLKEAVEDADLLIFVIPHQFLESVLSQIKENNNLKKHARAISLTKGII 133
Query: 90 QEASEAYLV 98
E + L
Sbjct: 134 VENGKPVLC 142
>gnl|CDD|234474 TIGR04113, cas_csx17, CRISPR-associated protein Csx17, subtype
Dpsyc. Members of this protein family are found
exclusively in CRISPR-associated (cas) type I system
gene clusters of the Dpsyc subtype. Markers for that
type include a variant form of cas3 (model TIGR02621)
and the GSU0054-like protein family (model TIGR02165).
This family occurs in less than half of known Dpsyc
clusters.
Length = 704
Score = 26.2 bits (58), Expect = 7.2
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 50 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLV 98
R Q +L+ + R +D K F SA ++EA A
Sbjct: 371 RRQPRADLINELDGWLNRFRSFPRDGKAPASFLSAR-RRIEEAIFAAAT 418
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 25.8 bits (57), Expect = 7.3
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 64 FQRLVREIAQDFKTDLRFQSAAIGA 88
FQR+V IA +F DL SA A
Sbjct: 225 FQRIVMPIAYEFDPDLVIISAGFDA 249
>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 = 24.6 bits (54), Expect = 7.7
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 80 RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 124
+ +A+ L + +++Y+ L A HA R D+ L
Sbjct: 23 SAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDVVLT 67
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 26.1 bits (57), Expect = 8.0
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 54 STELLIRKLPFQRLVR 69
STE +++ LPFQRL R
Sbjct: 437 STEKVLKSLPFQRLKR 452
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 26.0 bits (58), Expect = 8.0
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEA 95
E LI K+ F R+ ++A+ K R+Q A+ AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
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 0.131 0.357
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,598,305
Number of extensions: 579156
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 563
Number of HSP's successfully gapped: 57
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.9 bits)
S2: 53 (24.3 bits)