RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1398
(102 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 146 bits (371), Expect = 4e-47
Identities = 72/82 (87%), Positives = 76/82 (92%)
Query: 4 VARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFE 63
VA ++ KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFE
Sbjct: 47 VALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFE 106
Query: 64 DTNLCAIHAKRVTIMPKDIQLA 85
DTNLCAIHAKRVTIMPKDIQLA
Sbjct: 107 DTNLCAIHAKRVTIMPKDIQLA 128
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 132 bits (335), Expect = 5e-42
Identities = 68/84 (80%), Positives = 72/84 (85%), Gaps = 2/84 (2%)
Query: 4 VARERFQKPMKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGL 61
VA +K KST+LLIRK PFQRLVREIAQ F T DLRFQSSA+MALQEA+EAYLVGL
Sbjct: 14 VALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGL 73
Query: 62 FEDTNLCAIHAKRVTIMPKDIQLA 85
FEDTNL AIHAKRVTIMPKDIQLA
Sbjct: 74 FEDTNLLAIHAKRVTIMPKDIQLA 97
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 133 bits (336), Expect = 7e-42
Identities = 73/82 (89%), Positives = 76/82 (92%)
Query: 4 VARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFE 63
VA +K KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAV+ALQEA+EAYLVGLFE
Sbjct: 47 VALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFE 106
Query: 64 DTNLCAIHAKRVTIMPKDIQLA 85
DTNLCAIHAKRVTIMPKDIQLA
Sbjct: 107 DTNLCAIHAKRVTIMPKDIQLA 128
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 99 bits (250), Expect = 2e-29
Identities = 40/72 (55%), Positives = 48/72 (66%)
Query: 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 74
S+ LLI KLPF R+VRE+ + F +LR S A +ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 75 VTIMPKDIQLAA 86
TI P+DIQLA
Sbjct: 61 KTITPRDIQLAV 72
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 97.8 bits (243), Expect = 8e-28
Identities = 54/83 (65%), Positives = 65/83 (78%), Gaps = 1/83 (1%)
Query: 4 VARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVMALQEASEAYLVGLF 62
VA +K KSTELLIRKLPF RLVREI+ + + R+ + A++ALQEA+E +LV LF
Sbjct: 40 VALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLF 99
Query: 63 EDTNLCAIHAKRVTIMPKDIQLA 85
ED NLCAIHAKRVTIMPKD+QLA
Sbjct: 100 EDCNLCAIHAKRVTIMPKDMQLA 122
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 95.9 bits (238), Expect = 2e-27
Identities = 52/73 (71%), Positives = 63/73 (86%), Gaps = 1/73 (1%)
Query: 14 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHA 72
KST+LLIR+LPF RLVREI + + R+Q SA++ALQEA+EA+LVGLFED+NLCAIH
Sbjct: 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHG 75
Query: 73 KRVTIMPKDIQLA 85
KRVTIMPKD+QLA
Sbjct: 76 KRVTIMPKDMQLA 88
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 88.9 bits (221), Expect = 7e-25
Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 5/83 (6%)
Query: 4 VARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFE 63
V + ++ +ST+LL+ K P +R++R+ + R SSA+ LQEA E YL + E
Sbjct: 4 VGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEEIAE 58
Query: 64 DTNLCAIHAKRVTIMPKDIQLAA 86
D A HAKR T+ +DI+LA
Sbjct: 59 DAVELAEHAKRKTVKAEDIKLAL 81
>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 = 28.9 bits (65), Expect = 0.15
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 16 TELLIRKLPFQRLVREIAQDFKT 38
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 29.9 bits (68), Expect = 0.17
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA 56
E LI K+ F R+ ++A+ K R+Q AV+AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
>gnl|CDD|215271 PLN02491, PLN02491, carotenoid 9,10(9',10')-cleavage dioxygenase.
Length = 545
Score = 28.3 bits (63), Expect = 0.67
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 38 TDLRFQSSAVMALQEASEAYLVGLFEDTNL 67
T L + ++AL EA + Y+V + ED +L
Sbjct: 178 TALIYHHGKLLALSEADKPYVVKVLEDGDL 207
>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 = 0.73
Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 3/54 (5%)
Query: 30 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 83
++ Q F + Q + E L + + I AK + + K
Sbjct: 201 TDLPQIFD---KLQELDEKRINRTVELLLQAAEIERKVIPIIAKCLDGIKKAGD 251
>gnl|CDD|111209 pfam02291, TFIID-31kDa, Transcription initiation factor IID, 31kD
subunit. This family represents the N-terminus of the
31kD subunit (42kD in drosophila) of transcription
initiation factor IID (TAFII31). TAFII31 binds to p53,
and is an essential requirement for p53 mediated
transcription activation.
Length = 129
Score = 27.1 bits (60), Expect = 1.2
Identities = 10/47 (21%), Positives = 25/47 (53%)
Query: 42 FQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88
++ V+ L + + Y + +D + + HA++ I +D++LA +
Sbjct: 30 YEPRVVLQLLDFAHRYTQKILQDAKVYSRHARKANIDAEDVRLAIAA 76
>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 = 26.9 bits (60), Expect = 1.7
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 18/60 (30%)
Query: 29 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88
+ +A+D + LR +QEA++ H+KR + D+ A
Sbjct: 22 AQLLAEDVEYRLR------EIIQEAAK------------FMRHSKRRKLTTSDVNHALRL 63
>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 = 26.4 bits (59), Expect = 1.9
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 56 AYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88
Y + +D + + HA + I D++LA +S
Sbjct: 33 RYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65
>gnl|CDD|220619 pfam10182, Flo11, Flo11 domain. This presumed domain is found at
the N-terminus of the S. cerevisiae Flo11 protein.
Flo11 is required for diploid pseudohyphal formation
and haploid invasive growth. It belongs to a family of
proteins involved in invasive growth, cell-cell
adhesion, and mating, many of which can substitute for
each other under abnormal conditions.
Length = 152
Score = 25.8 bits (57), Expect = 3.2
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 36 FKTDLRFQSSAVMALQEASEAYLVGL 61
+K + FQ+ + L+ ++GL
Sbjct: 35 YKVTIHFQTQVSIPLKSLKSLKIIGL 60
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 26.1 bits (58), Expect = 3.2
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 10/64 (15%)
Query: 6 RERFQKPMKSTELLIRKLP-----FQRLVREIAQDFKTDL---RF--QSSAVMALQEASE 55
+ L + P ++LV I+ DF TDL RF AV L+E +E
Sbjct: 188 DQELISCQSLETLFQERFPQALDNLEKLVSGISYDFDTDLKLPRFNRDRPAVEELRELAE 247
Query: 56 AYLV 59
L
Sbjct: 248 LGLK 251
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 24.5 bits (54), Expect = 5.2
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 16 TELLIRKLPFQRLVREIAQDFKT 38
T+L++R +PF+ +E+ + F
Sbjct: 1 TKLIVRNVPFEATKKELRELFSP 23
>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 = 24.5 bits (54), Expect = 5.4
Identities = 15/62 (24%), Positives = 29/62 (46%)
Query: 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
+R ++E+ ++ + L E ++ ++ + ED A H K T+ KD+QL
Sbjct: 4 KRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLH 63
Query: 86 AE 87
E
Sbjct: 64 LE 65
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 25.7 bits (56), Expect = 5.9
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 15 STELLIRKLPFQRLVR 30
STE +++ LPFQRL R
Sbjct: 437 STEKVLKSLPFQRLKR 452
>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 = 6.3
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
+LP R V+ I + R A + E E ++ + + KR TI +
Sbjct: 1 AELPIAR-VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59
Query: 81 DIQLA 85
I+LA
Sbjct: 60 HIKLA 64
>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 = 24.2 bits (53), Expect = 7.4
Identities = 11/45 (24%), Positives = 19/45 (42%)
Query: 41 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
+ SA+ L + +++Y+ L A HA R D+ L
Sbjct: 23 SAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDVVLT 67
>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 = 25.2 bits (55), Expect = 7.6
Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 14/90 (15%)
Query: 8 RFQKPMKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSSAVMALQEASEAYLVGLFEDTN 66
R ++S + + R++ I + L + ++ + A Y FE +
Sbjct: 333 RLSNILRSNQDT-----YMRILWYILSNGGAEFL----ATLLKPEYAEYNYT---FEGLD 380
Query: 67 LCAIHAKRVTIMPKDIQLAAESVENARLRI 96
+ + + V+ P++ + A+S R+RI
Sbjct: 381 IGTLFGEIVSKTPRNTK-RADSEAARRVRI 409
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 24.9 bits (54), Expect = 8.8
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 6/36 (16%)
Query: 69 AIHAKRVTIMPKDIQ--LAAESVENARLRIRLISTP 102
A+H K++ ++++ L A+ +ENA RI LI+ P
Sbjct: 87 AVHKKKI----EEVETWLKAQVLENAPKRILLITGP 118
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae
Stress-seventy subfamily Q protein 1/Ssq1p (also called
Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae
Stress-Seventy subfamily C/Ssc1p (also called mtHSP70,
Endonuclease SceI 75 kDa subunit). It belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly, and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively.
Length = 376
Score = 24.9 bits (55), Expect = 9.3
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 26 QRLVREIAQDFK----TDLRFQSSAVMALQEASE 55
QR++ + ++FK DLR A+ L+EA+E
Sbjct: 228 QRIIDWLVEEFKKEEGIDLRKDKMALQRLKEAAE 261
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
0.324 0.133 0.370
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,075,726
Number of extensions: 410682
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 38
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)