RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2968
(173 letters)
>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 505
Score = 86.6 bits (215), Expect = 2e-20
Identities = 35/75 (46%), Positives = 53/75 (70%)
Query: 2 SIAIFFTLAASLLPWIAYYVANWQYLCVITSLPLLVAVITPWIVPESARWLVSQGRVDEA 61
I +FF+L LLP +AY++ +W++L + SLP + + W VPES RWL+SQGR++EA
Sbjct: 220 LIQVFFSLGLVLLPLVAYFIPDWRWLQLAVSLPTFLFFLLSWFVPESPRWLISQGRIEEA 279
Query: 62 VVIMKRFEKINNKKV 76
+ I++R KIN KK+
Sbjct: 280 LKILQRIAKINGKKL 294
Score = 50.0 bits (120), Expect = 1e-07
Identities = 18/39 (46%), Positives = 23/39 (58%)
Query: 101 YSAVINPKLPLIILGMIGILGGALCLFLPETLGQDLPQT 139
Y LPL++ G + +L G L LFLPET G LP+T
Sbjct: 467 YLGEKWLFLPLVLFGGLALLAGILTLFLPETKGVPLPET 505
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 39.2 bits (91), Expect = 6e-04
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 18 AYYVANWQYLCVITSLPLLVAVITPWIVPESARWLVSQGRVDEAVVIMKRFEKIN 72
AY +W+ ++ + P + A+ +PES R+ + G+ DEA +I+K N
Sbjct: 327 AYQFHSWRVFVIVCAFPCVFAIGALTFMPESPRFFLENGKHDEAWMILKLIHDTN 381
>gnl|CDD|182225 PRK10077, xylE, D-xylose transporter XylE; Provisional.
Length = 479
Score = 38.5 bits (90), Expect = 0.001
Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 24 WQYLCVITSLPLLVAVITPWIVPESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQ 83
W+Y+ ++P L+ ++ + VPE+ R+L+S+G+ ++A I+ KI + + Q+
Sbjct: 193 WRYMFASEAIPALLFLMLLYFVPETPRYLMSRGKQEQAEGIL---RKIMGNTLATQALQE 249
Query: 84 LKETCQRQAK 93
+K + K
Sbjct: 250 IKHSLDHGRK 259
>gnl|CDD|233165 TIGR00879, SP, MFS transporter, sugar porter (SP) family. This
model represent the sugar porter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 481
Score = 36.9 bits (86), Expect = 0.003
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 2 SIAIFFTLAASLLPWIAYYVANWQ---YLCVITSLPLLVAVITPWIVPESARWLVSQGRV 58
+ I W+ L +I + L + + +PES RWLV +GRV
Sbjct: 173 TFGILVAYGFGSGKVSLNNTLGWRIPLGLQLIPAGLLFLGLFF---LPESPRWLVGKGRV 229
Query: 59 DEA 61
+EA
Sbjct: 230 EEA 232
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 35.7 bits (83), Expect = 0.007
Identities = 22/124 (17%), Positives = 48/124 (38%), Gaps = 18/124 (14%)
Query: 3 IAIFFTLAASLLPWIAYYVANWQY-----LCVITSLPLLVAVITPWIVPESARWLVSQGR 57
+A L + Y + + L + ++ LL+ + +PES RWLV +G+
Sbjct: 152 VAAIIGLG------LNKYSNSDGWRIPLGLQFVPAILLLIGL---LFLPESPRWLVLKGK 202
Query: 58 VDEAVVIMKRFEKINN-KKVDPKLYQQLKETCQRQAKQEIDGKRYSAVINPKLPLIILGM 116
++EA K+ VD ++ ++ + ++ + L++ M
Sbjct: 203 LEEA---RAVLAKLRGVSDVDQEIQEEKDSLERSVEAEKASWLELFRGKTVRQRLLMGVM 259
Query: 117 IGIL 120
+ I
Sbjct: 260 LQIF 263
>gnl|CDD|233175 TIGR00895, 2A0115, benzoate transport. [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 398
Score = 31.6 bits (72), Expect = 0.19
Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 16/94 (17%)
Query: 8 TLAASLLPWIAYYVANWQYLCVI-TSLPLLVAVITPWIVPESARWLVSQGRVDEAVVIMK 66
LA L+P W+ L + PLL+ ++ +PES +LVS+
Sbjct: 159 FLAGWLIPVFG-----WRSLFYVGGIAPLLLLLLLMRFLPESIDFLVSKRPETVR----- 208
Query: 67 RFEKINNKKVDPKLYQQLKETCQRQAKQEIDGKR 100
+I N + + K KR
Sbjct: 209 ---RIVNAIAPQMQAEAQSAL--PEQKATQGTKR 237
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 29.5 bits (67), Expect = 0.79
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 44 IVPESARWLV--SQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQAKQ----EID 97
++ E A +LV R + + + RFEKI+N + +Q K +C + E+
Sbjct: 196 VLFERATFLVISHSSRKEASALDPHRFEKISN------IIKQFKLSCSKLQASFQSMEVR 249
Query: 98 GKRYSAVINP 107
+SA I+
Sbjct: 250 NSNFSAFIDE 259
>gnl|CDD|238504 cd01031, EriC, ClC chloride channel EriC. This domain is found in
the EriC chloride transporters that mediate the extreme
acid resistance response in eubacteria and archaea. This
response allows bacteria to survive in the acidic
environments by decarboxylation-linked proton
utilization. As shown for Escherichia coli EriC, these
channels can counterbalance the electric current
produced by the outwardly directed virtual proton pump
linked to amino acid decarboxylation. The EriC proteins
belong to the ClC superfamily of chloride ion channels,
which share a unique double-barreled architecture and
voltage-dependent gating mechanism. The
voltage-dependent gating is conferred by the permeating
anion itself, acting as the gating charge. In
Escherichia coli EriC, a glutamate residue that
protrudes into the pore is thought to participate in
gating by binding to a Cl- ion site within the
selectivity filter.
Length = 402
Score = 29.4 bits (67), Expect = 0.97
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 105 INPKLPLIILGMIGILGGALCLFLPETLG 133
+ + + + G+L G L L LPE LG
Sbjct: 238 LKKLPRELRVLLPGLLIGPLGLLLPEALG 266
>gnl|CDD|224744 COG1831, COG1831, Predicted metal-dependent hydrolase (urease
superfamily) [General function prediction only].
Length = 285
Score = 29.3 bits (66), Expect = 0.97
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 38 AVITPWIVPESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKE 86
AV+ P VP R ++ +G + E V +I+ + + ++Y E
Sbjct: 243 AVLGPKTVPRRTREILEKGDLTEEDV-----YRIHVENPE-RVYGIELE 285
>gnl|CDD|225817 COG3278, CcoN, Cbb3-type cytochrome oxidase, subunit 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 482
Score = 29.3 bits (66), Expect = 1.1
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 3 IAIFFTLAASLLPWIAYYVANWQYLCVITSLPLL 36
I F T+ P I YVANW Y I ++ +L
Sbjct: 146 IVFFGTILKRKEPHI--YVANWFYGAFIVTIAML 177
>gnl|CDD|214016 cd12923, iSH2_PI3K_IA_R, Inter-Src homology 2 (iSH2) helical domain
of Class IA Phosphoinositide 3-kinase Regulatory
subunits. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of the
inositol ring of D-myo-phosphatidylinositol (PtdIns) or
its derivatives. They play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation, and apoptosis. They
are classified according to their substrate specificity,
regulation, and domain structure. Class IA PI3Ks are
heterodimers of a p110 catalytic (C) subunit and a
p85-related regulatory (R) subunit. The R subunit
down-regulates PI3K basal activity, stabilizes the C
subunit, and plays a role in the activation downstream
of tyrosine kinases. All R subunits contain two SH2
domains that flank an intervening helical domain (iSH2),
which binds to the N-terminal adaptor-binding domain
(ABD) of the catalytic subunit. In vertebrates, there
are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode
for different Class IA PI3K R subunits.
Length = 152
Score = 27.6 bits (62), Expect = 2.2
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 59 DEAVVIMKRFEKINNKKVD-PKLYQQLKETCQRQAKQEIDGKR 100
E + K+ ++IN + +D + Y +L E + QEI KR
Sbjct: 3 VEKLA--KKLKEINKEYLDKSREYDELYEKYNK-LSQEIQLKR 42
>gnl|CDD|182478 PRK10461, PRK10461, thiamine biosynthesis lipoprotein ApbE;
Provisional.
Length = 350
Score = 28.2 bits (63), Expect = 2.3
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 95 EIDGKRYSAVINP 107
E+DGKR S VI+P
Sbjct: 263 ELDGKRLSHVIDP 275
>gnl|CDD|217315 pfam03006, HlyIII, Haemolysin-III related. Members of this family
are integral membrane proteins. This family includes a
protein with hemolytic activity from Bacillus cereus. It
has been proposed that YOL002c encodes a Saccharomyces
cerevisiae protein that plays a key role in metabolic
pathways that regulate lipid and phosphate metabolism.
In eukaryotes, members are seven-transmembrane pass
molecules found to encode functional receptors with a
broad range of apparent ligand specificities, including
progestin and adipoQ receptors, and hence have been
named PAQR proteins. The mammalian members include
progesterone binding proteins. Unlike the case with GPCR
receptor proteins, the evolutionary ancestry of the
members of this family can be traced back to the
Archaea.
Length = 207
Score = 28.0 bits (63), Expect = 2.5
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 4 AIFFTLAASLLPWIAYYVANWQYLCVITSLPLL--VAVITPWIVPESARWL 52
I+ +A S P++ Y + ++ + L + ++ + RWL
Sbjct: 82 GIYLLIAGSYTPFLLYALCGPLGWILLIFIWGLALLGILLKLFWLKRFRWL 132
>gnl|CDD|217678 pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This
family contains uncharacterized integral membrane
proteins.
Length = 771
Score = 28.3 bits (64), Expect = 2.7
Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 3 IAIFFTLAASLLPWIAYYVANWQYLCVITSLPLLVAVITPWIVPESARWLVSQGRV 58
I L ++L + + W+ + +L +++A++ + P LV Q V
Sbjct: 248 ILAVIALLVAVLFFANIFRRKWRLPAIALALLVVLAILLGGVYP----ALVQQFVV 299
>gnl|CDD|225937 COG3402, COG3402, Uncharacterized conserved protein [Function
unknown].
Length = 161
Score = 27.4 bits (61), Expect = 3.1
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 1 MSIAIFFTLAASLLPWIAYYVANWQYLCVITS--LPLLVAVITPWIVPESARWLV 53
+ IA+ +A + Y+V + + + LL AV+T +I+P+ R+ V
Sbjct: 23 IPIALVLLIAVAAGVL-LYFVGLDPNWSSVAAVAVILLAAVVTLFIIPQLVRYRV 76
>gnl|CDD|238831 cd01661, cbb3_Oxidase_I, Cytochrome cbb3 oxidase subunit I.
Cytochrome cbb3 oxidase, the terminal oxidase in the
respiratory chains of proteobacteria, is a multi-chain
transmembrane protein located in the cell membrane. Like
other cytochrome oxidases, it catalyzes the reduction of
O2 and simultaneously pumps protons across the membrane.
Found mainly in proteobacteria, cbb3 is believed to be
a modern enzyme that has evolved independently to
perform a specialized function in microaerobic energy
metabolism. Subunit I contains a heme-copper binuclear
center (the active site where O2 is reduced to water)
formed by a high-spin heme and a copper ion. It also
contains a low-spin heme, believed to participate in the
transfer of electrons to the binuclear center. The cbb3
operon contains four genes (ccoNOQP or fixNOQP), with
ccoN coding for subunit I. Instead of a CuA-containing
subunit II analogous to other cytochrome oxidases, cbb3
utilizes subunits ccoO and ccoP, which contain one and
two hemes, respectively, to transfer electrons to the
binuclear center. The fourth subunit (ccoQ) has been
shown to protect the core complex from proteolytic
degradation by serine proteases. For every reduction of
an O2 molecule, eight protons are taken from the inside
aqueous compartment and four electrons are taken from
cytochrome c on the opposite side of the membrane. The
four electrons and four of the protons are used in the
reduction of O2; the four remaining protons are pumped
across the membrane. This charge separation of four
charges contributes to the electrochemical gradient used
for ATP synthesis. The polar residues that form the D-
and K-pathways in subunit I of other cytochrome c and
ubiquinol oxidases are absent in cbb3. The proton
pathways remain undefined. A pathway for the transfer
of pumped protons beyond the binuclear center also
remains undefined. It is believed that electrons are
passed from cytochrome c (the electron donor) to the
low-spin heme via ccoP and ccoO, respectively, and
directly from the low-spin heme to the binuclear center.
Length = 493
Score = 27.7 bits (62), Expect = 3.6
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 7 FTLAASLLPWIAYYVANWQYLCVITSLPLL 36
TL P I YVANW YL I ++ +L
Sbjct: 180 GTLLRRKEPHI--YVANWYYLAFIVTVAVL 207
>gnl|CDD|224040 COG1115, AlsT, Na+/alanine symporter [Amino acid transport and
metabolism].
Length = 452
Score = 27.5 bits (62), Expect = 3.9
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 2 SIAIFFTLAASLLPWIAYYVANWQYLC 28
+IA+F ++L W Y N ++L
Sbjct: 356 AIALFLFAFTTILGWYYYGEKNIEFLF 382
>gnl|CDD|133023 cd04180, UGPase_euk_like, Eukaryotic UGPase-like includes UDPase
and UDPGlcNAc pyrophosphorylase enzymes. This family
includes UDP-Glucose Pyrophosphorylase (UDPase) and
UDPGlcNAc pyrophosphorylase enzymes. The two enzymes
share significant sequence and structure similarity.
UDP-Glucose Pyrophosphorylase catalyzes a reversible
production of UDP-Glucose and pyrophosphate (PPi) from
Glucose-1-phosphate and UTP. UDP-glucose plays pivotal
roles in galactose utilization, in glycogen synthesis,
and in the synthesis of the carbohydrate moieties of
glycolipids , glycoproteins , and proteoglycans .
UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylase
(UAP) (also named GlcNAc1P uridyltransferase), catalyzes
the reversible conversion of UTP and GlcNAc1P from PPi
and UDPGlcNAc, which is a key precursor of N- and
O-linked glycosylations and is essential for the
synthesis of chitin (a major component of the fungal
cell wall) and of the glycosylphosphatidylinositol (GPI)
linker anchoring a variety of cell surface proteins to
the plasma membrane. In bacteria, UDPGlcNAc represents
an essential precursor for both peptidoglycan and
lipopolysaccharide biosynthesis.
Length = 266
Score = 27.1 bits (60), Expect = 5.1
Identities = 9/40 (22%), Positives = 13/40 (32%)
Query: 68 FEKINNKKVDPKLYQQLKETCQRQAKQEIDGKRYSAVINP 107
FEKIN K + Q K + + + P
Sbjct: 72 FEKINQKNSYVITFMQGKLPLKNDDDARDPHNKTKCHLFP 111
>gnl|CDD|111006 pfam02064, MAS20, MAS20 protein import receptor.
Length = 184
Score = 27.0 bits (59), Expect = 5.3
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 74 KKVDPKLYQQLKETCQRQAKQEIDGKRYS 102
++ DP+ +QL++ + QAK E + ++
Sbjct: 33 RRNDPEFRKQLRQRAKEQAKMEEEAAEHA 61
>gnl|CDD|185264 PRK15366, PRK15366, type III secretion system chaperone SsaE;
Provisional.
Length = 80
Score = 25.7 bits (56), Expect = 6.3
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 46 PESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQQ 83
E A+ ++ Q R K+ E+ N K DP+ YQQ
Sbjct: 15 REEAKGIILQLRA-----ARKQLEENNGKLQDPQQYQQ 47
>gnl|CDD|232854 TIGR00170, leuC, 3-isopropylmalate dehydratase, large subunit.
Members of this family are 3-isopropylmalate
dehydratase, large subunit, or the large subunit domain
of single-chain forms. Homoaconitase, aconitase, and
3-isopropylmalate dehydratase have similar overall
structures. All are dehydratases (EC 4.2.1.-) and bind a
Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase
is split into large (leuC) and small (leuD) chains in
eubacteria. Several pairs of archaeal proteins resemble
the leuC and leuD pair in length and sequence but even
more closely resemble the respective domains of
homoaconitase, and their identity is uncertain. These
homologs are now described by a separate model of
subfamily (rather than equivalog) homology type, and the
priors and cutoffs for this model have been changed to
focus this equivalog family more narrowly [Amino acid
biosynthesis, Pyruvate family].
Length = 465
Score = 26.7 bits (59), Expect = 6.5
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 82 QQLKETCQRQAKQEIDGKRYSAVINPKLPLIILGMIGILGGALCL 126
Q LK+ + K E+DGK + + L I+G G+ GG +
Sbjct: 156 QTLKQARAKTMKIEVDGKLAPGITAKDIILAIIGKTGVAGGTGHV 200
>gnl|CDD|201407 pfam00707, IF3_C, Translation initiation factor IF-3, C-terminal
domain.
Length = 87
Score = 25.5 bits (57), Expect = 7.0
Identities = 4/30 (13%), Positives = 16/30 (53%)
Query: 79 KLYQQLKETCQRQAKQEIDGKRYSAVINPK 108
+ + L++ + +++G+ + ++ PK
Sbjct: 58 RFAEDLEDIATVEKPPKMEGRNMTMILAPK 87
>gnl|CDD|178172 PLN02557, PLN02557, phosphoribosylformylglycinamidine cyclo-ligase.
Length = 379
Score = 26.7 bits (59), Expect = 7.6
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 43 WIVPESARWLVSQGRVDEA 61
W VP +WL G +++A
Sbjct: 314 WEVPPLFKWLQEAGNIEDA 332
>gnl|CDD|225350 COG2740, COG2740, Predicted nucleic-acid-binding protein
implicated in transcription termination
[Transcription].
Length = 95
Score = 25.4 bits (56), Expect = 8.0
Identities = 7/29 (24%), Positives = 10/29 (34%)
Query: 66 KRFEKINNKKVDPKLYQQLKETCQRQAKQ 94
K F + KV LY +L +
Sbjct: 63 KLFSRALKAKVSDSLYDELIQLLAELEPP 91
>gnl|CDD|235659 PRK05974, PRK05974, phosphoribosylformylglycinamidine synthase
subunit PurS; Reviewed.
Length = 80
Score = 25.2 bits (56), Expect = 8.5
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 60 EAVVIMKRFEKINNKKVDPKLYQQLKETCQR 90
E V K FE + + K LKE C++
Sbjct: 34 EDVRQGKYFELELEGESEEKAEADLKEMCEK 64
>gnl|CDD|173966 cd08047, TAF7, TATA Binding Protein (TBP) Associated Factor 7
(TAF7) 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 7 (TAF7) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(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
preinitiation 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. Each TAF, with the
help of a specific activator, is required only for
expression of subset of genes and is not universally
involved for transcription as are GTFs. TAF7 is involved
in the regulation of the transition from PIC assembly to
initiation and elongation. 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.
Length = 162
Score = 25.7 bits (57), Expect = 9.7
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 69 EKINNKKVDPKLYQQLKETCQRQAKQEIDGKRYSAVINPKLPLII 113
+ I + KL R+A I+G++Y A + LP II
Sbjct: 18 KAIEEGDSNEKLLSITLFEDSRRAVVRINGQKYPAKL-VDLPTII 61
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
0.325 0.141 0.444
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,187,910
Number of extensions: 857530
Number of successful extensions: 1601
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1597
Number of HSP's successfully gapped: 63
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
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: 55 (24.8 bits)