RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17763
(136 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 242 bits (619), Expect = 3e-84
Identities = 130/136 (95%), Positives = 135/136 (99%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLA+KAARKSAP TGG+KKPHRYRPGTVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 120
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 121 MPKDIQLARRIRGERA 136
MPKDIQLARRIRGER+
Sbjct: 121 MPKDIQLARRIRGERS 136
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 217 bits (553), Expect = 3e-74
Identities = 133/136 (97%), Positives = 136/136 (100%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 120
LLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFEDTNLCAIHAKRVTI
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120
Query: 121 MPKDIQLARRIRGERA 136
MPKDIQLARRIRGERA
Sbjct: 121 MPKDIQLARRIRGERA 136
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 173 bits (440), Expect = 2e-57
Identities = 89/105 (84%), Positives = 93/105 (88%), Gaps = 2/105 (1%)
Query: 34 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVM 91
GG K RYRPG VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQSSA+M
Sbjct: 1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIM 60
Query: 92 ALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
ALQEA+EAYLVGLFEDTNL AIHAKRVTIMPKDIQLARRIRGER
Sbjct: 61 ALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGERL 105
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 138 bits (349), Expect = 2e-43
Identities = 83/134 (61%), Positives = 101/134 (75%), Gaps = 8/134 (5%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MAR Q ++ GK P+K+ + ++ KKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTE 53
Query: 61 LLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT 119
LLIRKLPF RLVREI+ + + R+ + A++ALQEA+E +LV LFED NLCAIHAKRVT
Sbjct: 54 LLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVT 113
Query: 120 IMPKDIQLARRIRG 133
IMPKD+QLARRIRG
Sbjct: 114 IMPKDMQLARRIRG 127
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 120 bits (301), Expect = 2e-36
Identities = 66/93 (70%), Positives = 80/93 (86%), Gaps = 1/93 (1%)
Query: 43 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYL 101
RPG AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q SA++ALQEA+EA+L
Sbjct: 2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHL 61
Query: 102 VGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134
VGLFED+NLCAIH KRVTIMPKD+QLARRIRG+
Sbjct: 62 VGLFEDSNLCAIHGKRVTIMPKDMQLARRIRGQ 94
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 103 bits (259), Expect = 4e-30
Identities = 41/75 (54%), Positives = 50/75 (66%)
Query: 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
S+ LLI KLPF R+VRE+ + F +LR S A +ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 118 VTIMPKDIQLARRIR 132
TI P+DIQLA R+
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 101 bits (253), Expect = 4e-29
Identities = 43/92 (46%), Positives = 58/92 (63%), Gaps = 5/92 (5%)
Query: 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVG 103
PG V L+EIRRYQ+ST+LL+ K P +R++R+ + R SSA+ LQEA E YL
Sbjct: 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEE 55
Query: 104 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
+ ED A HAKR T+ +DI+LA + G R
Sbjct: 56 IAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 30.3 bits (69), Expect = 0.28
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA 99
E LI K+ F R+ ++A+ K R+Q AV+AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
>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 = 29.6 bits (67), Expect = 0.41
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 18/62 (29%)
Query: 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
+ +A+D + LR +QEA++ H+KR + D+ A R+
Sbjct: 22 AQLLAEDVEYRLR------EIIQEAAK------------FMRHSKRRKLTTSDVNHALRL 63
Query: 132 RG 133
R
Sbjct: 64 RN 65
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 30.0 bits (67), Expect = 0.46
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 5 KQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHR 41
K A+K KAP K++A K A K A K R
Sbjct: 1014 KAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGR 1050
Score = 28.0 bits (62), Expect = 2.0
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 2 ARTKQTARKSTGGKAP------RKQLATKAARKSAPATGGVKKPHR 41
A K+ A+K+ KA +K A K K APA +KP
Sbjct: 991 AMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAA 1036
>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 = 0.49
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 59 TELLIRKLPFQRLVREIAQDFKT 81
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein
4 and similar proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. This subfamily is composed of
Cdc42-Interacting Protein 4 (CIP4), Formin Binding
Protein 17 (FBP17), FormiN Binding Protein 1-Like
(FNBP1L), and similar proteins. CIP4 and FNBP1L are
Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. Members of this subfamily typically
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. In addition, some members such as FNBP1L contain
a central Cdc42-binding HR1 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 251
Score = 28.0 bits (63), Expect = 1.5
Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 3/54 (5%)
Query: 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 126
++ Q F + Q + E L + + I AK + + K
Sbjct: 201 TDLPQIFD---KLQELDEKRINRTVELLLQAAEIERKVIPIIAKCLDGIKKAGD 251
>gnl|CDD|215271 PLN02491, PLN02491, carotenoid 9,10(9',10')-cleavage dioxygenase.
Length = 545
Score = 28.3 bits (63), Expect = 1.6
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNL 110
T L + ++AL EA + Y+V + ED +L
Sbjct: 178 TALIYHHGKLLALSEADKPYVVKVLEDGDL 207
>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 = 26.0 bits (58), Expect = 2.8
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM 121
++ K Q L++EI + L E ++ ++ + ED A H K T+
Sbjct: 1 ILTKRKLQELLKEIDPR----EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLE 56
Query: 122 PKDIQLA 128
KD+QL
Sbjct: 57 VKDVQLH 63
>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 = 27.0 bits (60), Expect = 3.3
Identities = 10/30 (33%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 11 STGGKAPRKQLATKAARKSAPATGGVKKPH 40
KAPR+QL K R KK
Sbjct: 467 FGNVKAPRQQLNIK--RPEESEESEGKKQS 494
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 27.2 bits (60), Expect = 3.6
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK 37
K A+K A K A +K+AP G+K
Sbjct: 882 PAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLK 917
>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 = 4.2
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 99 AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133
Y + +D + + HA + I D++LA + R
Sbjct: 33 RYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV 67
>gnl|CDD|225055 COG2144, COG2144, Selenophosphate synthetase-related proteins
[General function prediction only].
Length = 324
Score = 26.6 bits (59), Expect = 4.9
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 49 LREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 82
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 = 6.0
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 55 YQKSTELLIRKLP 67
YQ++TE L RKLP
Sbjct: 388 YQQATEFLCRKLP 400
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 26.5 bits (59), Expect = 6.2
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 48 ALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD------LRFQSSAVMALQEA 96
L + K +LL+ + QRL R+I Q + + + AL EA
Sbjct: 544 TLADYAPITKDPDLLVEHVR-QRLGRQITQQYLDEDGVLPVITLDPDLEAALAEA 597
>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 = 6.3
Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 19/88 (21%)
Query: 53 RRYQKSTELLIRKLP--FQRLVREIAQD-FKTDLRFQSSAVMALQEASEAYLVGLFEDTN 109
+R +R + R++ I + L + ++ + A Y FE +
Sbjct: 332 KRLSNI----LRSNQDTYMRILWYILSNGGAEFL----ATLLKPEYAEYNYT---FEGLD 380
Query: 110 LCAIHAKRVTIMPK-----DIQLARRIR 132
+ + + V+ P+ D + ARR+R
Sbjct: 381 IGTLFGEIVSKTPRNTKRADSEAARRVR 408
>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 = 25.0 bits (55), Expect = 6.4
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 84 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 128
+ SA+ L + +++Y+ L A HA R D+ L
Sbjct: 23 SAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDVVLT 67
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 26.1 bits (58), Expect = 7.1
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 71 LVREIAQDFKTDL---RF--QSSAVMALQEASEAYLV 102
LV I+ DF TDL RF AV L+E +E L
Sbjct: 215 LVSGISYDFDTDLKLPRFNRDRPAVEELRELAELGLK 251
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 26.1 bits (57), Expect = 8.6
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 58 STELLIRKLPFQRLVR 73
STE +++ LPFQRL R
Sbjct: 437 STEKVLKSLPFQRLKR 452
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 26.0 bits (56), Expect = 8.9
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 8 ARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKL 66
A + +G K PR+ +AR+S + PH P VALR + R Q+ L+ +L
Sbjct: 1689 APRRSGAKDPRQGQYCPSARRS-------EAPHSPSPRDVALRLLERQQELNRQLLLEL 1740
>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 = 24.1 bits (53), Expect = 9.9
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 123
+LP R V+ I + R A + E E ++ + + KR TI +
Sbjct: 1 AELPIAR-VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59
Query: 124 DIQLA 128
I+LA
Sbjct: 60 HIKLA 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
0.321 0.131 0.361
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: 6,843,882
Number of extensions: 602040
Number of successful extensions: 585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 65
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.7 bits)