RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14684
(357 letters)
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 59.1 bits (144), Expect = 1e-11
Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 216 IRDIRRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQF 275
+ RRR +N+ AA+ R+RK +I L +V+Q++ + L +E E L +E ++KS+
Sbjct: 4 EKRRRRRERNREAARRSRERKKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63
Query: 276 SQ 277
+
Sbjct: 64 EE 65
>gnl|CDD|201054 pfam00170, bZIP_1, bZIP transcription factor. The Pfam entry
includes the basic region and the leucine zipper region.
Length = 64
Score = 41.9 bits (99), Expect = 2e-05
Identities = 22/55 (40%), Positives = 36/55 (65%)
Query: 220 RRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQ 274
RRR KN+ AA+ R RK I L ++VK+++ + + L E E L +EC+++KS+
Sbjct: 8 RRRQKNREAARRSRLRKKAYIEELEEKVKELEAENKTLRSELERLKKECAKLKSE 62
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 36.1 bits (84), Expect = 0.002
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 220 RRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQE 267
RR +N AA+ R++K + L + VK+++++ L Q+ E L +E
Sbjct: 7 DRRRRNNEAARRSREKKKQREEELEERVKELEEENAQLRQKVEQLEKE 54
>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and
multimerization region of GCN4 and related proteins.
Basic leucine zipper (bZIP) transcription factors act in
networks of homo- and hetero-dimers in the regulation in
a diverse set of cellular pathways. Classical leucine
zippers have alpha helices with leucine residues 7 amino
acids apart, which stabilize dimerization with a
parallel leucine zipper domain. Dimerization creates a
pair of basic regions that bind DNA and undergo
conformational change. GCN4 was identified in
Saccharomyces cerevisiae from mutations in a deficiency
in activation with the general amino acid control
pathway. GCN4 encodes a trans-activator of amino acid
biosynthetic genes containing 2 acidic activation
domains and a C-terminal bZIP domain, comprised of a
basic alpha-helical DNA-binding region and a coiled-coil
dimerization region.
Length = 54
Score = 33.4 bits (77), Expect = 0.012
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 216 IRDIRRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQ 274
R+R +N+ AA+ R RK+ + +KQ++DK L E+ L E R+K
Sbjct: 1 DPRARKRARNREAARRSRARKM-------ERMKQLEDKVEELTSENSDLEDEVDRLKKA 52
>gnl|CDD|185085 PRK15131, PRK15131, mannose-6-phosphate isomerase; Provisional.
Length = 389
Score = 34.9 bits (81), Expect = 0.056
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 150 TAKYI---EKLKMVDFAARKSEEEQMTRDEKKARALNIPIPVNDIINLPMDEFNERLSKY 206
T KYI E + V F A K + +T+ K+ L+ PIPV+D S +
Sbjct: 278 TPKYIDIPELVANVKFEA-KPANQLLTQPVKQGAELDFPIPVDDFA----------FSLH 326
Query: 207 DLSETQLSL 215
DLS+ +L
Sbjct: 327 DLSDQPTTL 335
>gnl|CDD|190534 pfam03131, bZIP_Maf, bZIP Maf transcription factor. Maf
transcription factors contain a conserved basic region
leucine zipper (bZIP) domain, which mediates their
dimerisation and DNA binding property. Thus, this family
is probably related to pfam00170.
Length = 93
Score = 30.8 bits (70), Expect = 0.22
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 220 RRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRV 271
RR KN+ AQ+CR +++ Q L E K L Q+ E L QE SR+
Sbjct: 33 RRTLKNRGYAQSCRSKRVQQRHELEKE-------KSQLQQQVEQLKQEVSRL 77
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 32.7 bits (75), Expect = 0.32
Identities = 25/131 (19%), Positives = 48/131 (36%), Gaps = 20/131 (15%)
Query: 161 DFAARKSEEEQMTRDEKKARALNIPIPVND---------------IINLPMDEFNERLSK 205
D A +S+ ++ + + RA + +I F R S
Sbjct: 82 DAAELESQVLRLEAEVARLRAEADSQAAIEFPDDLLSAEDPAVPELIKGQQSLFESRKST 141
Query: 206 YDLSETQLSLIRDIRRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDK--KRHLMQEHEY 263
QL LI ++ + ++A + + L Q L + E + + K ++ L+ E
Sbjct: 142 LRA---QLELILAQIKQLEAELAGLQAQLQALRQQLEVISEELEARRKLKEKGLVSRLEL 198
Query: 264 LSQECSRVKSQ 274
L E R ++Q
Sbjct: 199 LELERERAEAQ 209
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 31.7 bits (73), Expect = 0.58
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 233 RKRKL-DQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQL 278
R L ++ L ++++Q++ K R L E+E L +E R+KS+ +L
Sbjct: 2 RLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKL 48
>gnl|CDD|184143 PRK13561, PRK13561, putative diguanylate cyclase; Provisional.
Length = 651
Score = 31.2 bits (71), Expect = 0.99
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 24/92 (26%)
Query: 181 ALNIPIPVNDI-------INLPMDEFNERLSKYDLSETQLSLIRDIRRRGKNKVAAQNCR 233
+N +P+ I I + M F L+ L +S RR+GKN
Sbjct: 333 IINERLPIQRIQLRPSCSIGIAM--FYGDLTAEQLYSRAISAAFTARRKGKN-------- 382
Query: 234 KRKLDQILSLADEVKQMKDKKRHLMQEHEYLS 265
QI + +QM+ ++ L +E + L+
Sbjct: 383 -----QIQFF--DPQQMEAAQKRLTEESDILN 407
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 30.8 bits (69), Expect = 1.5
Identities = 26/127 (20%), Positives = 41/127 (32%), Gaps = 8/127 (6%)
Query: 163 AARKSEEEQMTRDEKKARALNIPIPVNDIINLPMDEFNERLSKYDLSETQLSLIRDIRRR 222
AA + +EQMT K A I + L K + L R+
Sbjct: 478 AAAERSQEQMTAALKALLAFQQQIADLSGAKEKASDQKSLLWKAEEQYALLKEEAKQRQL 537
Query: 223 GKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQLYKHV 282
+ + A +K L+ LA+ + Q D E +Q K + S LY+
Sbjct: 538 -QEQKALLEHKKETLEYTSQLAELLDQQAD-------RFELSAQAAGSQKERGSDLYREA 589
Query: 283 FNALRDS 289
+
Sbjct: 590 LAQNAAA 596
>gnl|CDD|222417 pfam13851, GAS, Growth-arrest specific micro-tubule binding. This
family is the highly conserved central region of a
number of metazoan proteins referred to as growth-arrest
proteins. In mouse, Gas8 is predominantly a testicular
protein, whose expression is developmentally regulated
during puberty and spermatogenesis. In humans, it is
absent in infertile males who lack the ability to
generate gametes. The localisation of Gas8 in the
motility apparatus of post-meiotic gametocytes and
mature spermatozoa, together with the detection of Gas8
also in cilia at the apical surfaces of epithelial cells
lining the pulmonary bronchi and Fallopian tubes
suggests that the Gas8 protein may have a role in the
functioning of motile cellular appendages. Gas8 is a
microtubule-binding protein localised to regions of
dynein regulation in mammalian cells.
Length = 201
Score = 29.5 bits (67), Expect = 2.1
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 11/74 (14%)
Query: 215 LIRDIRRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQ 274
L + ++ K+K + +N + R +K+++ + ++L E E L Q +V+ +
Sbjct: 74 LRKKLKDYEKDKQSLKNLKAR-----------LKELEKELKNLKWESEVLEQRFEKVERE 122
Query: 275 FSQLYKHVFNALRD 288
+LY A++D
Sbjct: 123 RDELYDKFEAAIQD 136
>gnl|CDD|226538 COG4052, COG4052, Uncharacterized protein related to methyl
coenzyme M reductase subunit C [General function
prediction only].
Length = 310
Score = 29.4 bits (66), Expect = 2.6
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 192 INLPMDEFNERLSKYDLSETQLSLIRDIRR 221
+ LP DE++E++++ ++ E L I DIRR
Sbjct: 260 VKLPYDEYHEKIAEVEVDEYVLGEIADIRR 289
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 29.7 bits (67), Expect = 2.7
Identities = 20/119 (16%), Positives = 36/119 (30%), Gaps = 16/119 (13%)
Query: 189 NDIINLPMDEFNERLSKYDL--SETQLSLIRD--------IRRRGKNKVAAQNCRKRKLD 238
N +E+ ER +E L+++ + R AAQ + L
Sbjct: 98 NPFSASLDEEYRERFEGERHFVNELYLTILYRPLPSLIGKLERYKNKLRAAQANTENDLK 157
Query: 239 QILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQLYKHVFNALRDSDGNPYSPF 297
+IL + ++DK ++ E + Y V L + Y
Sbjct: 158 EIL------RNLEDKTARVLALLRKYGPELLGNYEEDGLNYSEVLEFLAELINGGYLQP 210
>gnl|CDD|129633 TIGR00542, hxl6Piso_put, hexulose-6-phosphate isomerase, putative.
This family shows similarity by PSI-BLAST to other
isomerases. Putative identification as
hexulose-6-phosphate isomerase is reported in
Swiss-Prot, attributing a discussion in Genome Sci.
Technol. 1:53-75(1996). This family is conserved at
better than 40 % identity among the four known examples
from three species: Escherichia coli (SgbU and SgaU),
Haemophilus influenzae, and Mycoplasma pneumoniae. The
rarity of the family, high level of conservation, and
proposed catabolic role suggests lateral transfer may be
a part of the evolutionary history of this protein
[Energy metabolism, Sugars].
Length = 279
Score = 29.0 bits (65), Expect = 3.3
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 190 DIINLPMDEFNERLSKYDLSETQ-LSLIRDIRRRG 223
D + + +DE ++RLS+ D S Q L+L+ I G
Sbjct: 31 DFVEMSVDETDDRLSRLDWSREQRLALVNAIIETG 65
>gnl|CDD|222463 pfam13935, Ead_Ea22, Ead/Ea22-like protein. This family contains
phage proteins and bacterial proteins that are likely to
represent integrated phage proteins. This family
includes the Lambda phage Ea22 early protein as well as
the Bacteriophage P22 Ead protein.
Length = 143
Score = 28.4 bits (63), Expect = 3.4
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 227 VAAQNCRKRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQLYKHVFNA 285
+A N D +L+L DE+++ +D+ + E E V +L + A
Sbjct: 61 LAVANP-----DTVLALLDELEEYQDRIEAFEEVFEDAFIENEDVADDADELRDELEAA 114
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 29.4 bits (66), Expect = 3.4
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 234 KRKLD-QILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKS 273
+LD +I L DE + ++ +K L +E E L E R++S
Sbjct: 1 ISELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRS 41
>gnl|CDD|149487 pfam08440, Poty_PP, Potyviridae polyprotein. This domain is found
in polyproteins of the viral Potyviridae taxon.
Length = 274
Score = 28.3 bits (64), Expect = 5.1
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 118 LVSHNHTYSSSHSTSLAPETLGATSRNYSKDKTAKYIEKLKMV 160
S + SS S SL SR Y+KD T + I L+
Sbjct: 178 FKSVTSSSCSSSSFSLLSIANTIRSR-YAKDHTEENISVLQQA 219
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 28.4 bits (64), Expect = 5.3
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 12/101 (11%)
Query: 208 LSETQLSLIRDIR---RRGKN---KVAAQNCRKRKLDQILSLADEVKQMKDKK----RHL 257
+SE +++IR + G+ KV + ++ +D LSL + + KK +
Sbjct: 43 ISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHID--LSLKRVTEHQRRKKIQEWKKE 100
Query: 258 MQEHEYLSQECSRVKSQFSQLYKHVFNALRDSDGNPYSPFE 298
+ + L ++ + Y+ V L + G+ Y FE
Sbjct: 101 QKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFE 141
>gnl|CDD|234620 PRK00081, coaE, dephospho-CoA kinase; Reviewed.
Length = 194
Score = 27.7 bits (63), Expect = 6.3
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 14/34 (41%)
Query: 167 SEEE-------QMTRDEKKARALNIPIPVNDIIN 193
SEEE QM R+EK ARA +D+I+
Sbjct: 149 SEEEAEAIIASQMPREEKLARA-------DDVID 175
>gnl|CDD|203371 pfam06005, DUF904, Protein of unknown function (DUF904). This
family consists of several bacterial and archaeal
hypothetical proteins of unknown function.
Length = 72
Score = 26.1 bits (58), Expect = 6.4
Identities = 10/49 (20%), Positives = 28/49 (57%)
Query: 234 KRKLDQILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQLYKHV 282
++ ++ I L E++++K++ L +E+E L +E ++K + + +
Sbjct: 14 QQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNAWQSRL 62
>gnl|CDD|218099 pfam04465, DUF499, Protein of unknown function (DUF499). Family of
uncharacterized hypothetical prokaryotic proteins.
Length = 1025
Score = 28.7 bits (64), Expect = 6.6
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 196 MDEFNERLSKY--DLSETQLSLIRDIRRR 222
MDE E KY D+ Q S++ DIR R
Sbjct: 555 MDEIKEAYGKYGKDVVNIQKSMVEDIRDR 583
>gnl|CDD|166070 PLN02429, PLN02429, triosephosphate isomerase.
Length = 315
Score = 28.2 bits (62), Expect = 7.6
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 4/85 (4%)
Query: 9 HQYFYSMGSES----PASSGSHRIPPPAVAQKKYHLYGRRLFHDHNSTAASTSSDISSVD 64
HQ F+ + S +SS SHR P VA + N T S + IS ++
Sbjct: 30 HQSFFHRVNSSTRLVSSSSSSHRSPRGVVAMAGSGKFFVGGNWKCNGTKDSIAKLISDLN 89
Query: 65 SAAIKFEMNDTDSARLPMLDAASCS 89
SA ++ +++ S +D S
Sbjct: 90 SATLEADVDVVVSPPFVYIDQVKSS 114
>gnl|CDD|217630 pfam03592, Terminase_2, Terminase small subunit. Packaging of
double-stranded viral DNA concatemers requires
interaction of the prohead with virus DNA. This process
is mediated by a phage-encoded DNA recognition and
terminase protein. The terminase enzymes described so
far, which are hetero-oligomers composed of a small and
a large subunit, do not have a significant level of
sequence homology. The small terminase subunit is
thought to form a nucleoprotein structure that helps to
position the terminase large subunit at the packaging
initiation site.
Length = 141
Score = 27.3 bits (61), Expect = 7.7
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 142 SRNYSKDKTAKYIEKLKMVDFAARKSEEEQMTRDE 176
S +K K YI++L + + +T DE
Sbjct: 37 SELLTKPKIKAYIDELM-----KEREKRTIITADE 66
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR transcriptional
regulator proteins. The ros chromosomal gene is present
in octopine and nopaline strains of Agrobacterium
tumefaciens as well as in Rhizobium meliloti. This gene
encodes a 15.5-kDa protein that specifically represses
the virC and virD operons in the virulence region of the
Ti plasmid and is necessary for succinoglycan
production. Sinorhizobium meliloti can produce two types
of acidic exopolysaccharides, succinoglycan and
galactoglucan, that are interchangeable for infection of
alfalfa nodules. MucR from Sinorhizobium meliloti acts
as a transcriptional repressor that blocks the
expression of the exp genes responsible for
galactoglucan production therefore allowing the
exclusive production of succinoglycan.
Length = 130
Score = 27.1 bits (61), Expect = 7.8
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 238 DQILSLADEVKQMKDKKRHLMQEH 261
D I+ L D K+ K KRHL H
Sbjct: 69 DYIICLEDG-KKFKTLKRHLRTHH 91
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 28.1 bits (63), Expect = 8.3
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 197 DEFNERLSKYDLSETQLSLIRDIRRRGKNKVAAQNCRKRKLDQILSLADEVKQMKDKKRH 256
+E +++ + T K +VA + K +L+QI + ++K+ ++KR
Sbjct: 37 EELKQKVEEALEGATNEDGKLAADLL-KLEVARK---KERLNQIRARISQLKEEIEQKRE 92
Query: 257 LMQEH-EYLSQECSRVKSQFSQLYK 280
++E L+Q S + S QL K
Sbjct: 93 RIEELKRALAQRRSDLSSASYQLEK 117
>gnl|CDD|220212 pfam09376, NurA, NurA domain. This family includes NurA a nuclease
exhibiting both single-stranded endonuclease activity
and 5'-3' exonuclease activity on single-stranded and
double-stranded DNA from the hyperthermophilic archaeon
Sulfolobus acidocaldarius.
Length = 260
Score = 27.6 bits (61), Expect = 9.0
Identities = 19/95 (20%), Positives = 29/95 (30%), Gaps = 11/95 (11%)
Query: 161 DFAARKSEEEQMTRDEKKARALNIPIPVNDIINLPMD--------EFNERLSKYDLSETQ 212
+ R+ E M E A L + D+I +D E L +
Sbjct: 67 ELLLRRRVRELMALLELAAALLLLKEEGPDLI--LLDGSLIPTLIRLPEYLERILELLYL 124
Query: 213 LSLIRDIRRRGKNKVA-AQNCRKRKLDQILSLADE 246
L L+ G V + R +L +L E
Sbjct: 125 LRLLELALLEGIPLVGIVKTSRSSELLNLLRDELE 159
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 27.8 bits (62), Expect = 9.2
Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 239 QILSLADEVKQMKDKKRHLMQEHEYLSQECSRVKSQFSQLYKHVFNALRDSDGN 292
I + E+K + K + + +E + QE ++ ++ ++ K L D++ N
Sbjct: 285 SIEEVLSEIKALASKIKQVNEELTTVRQENEELEEEY-KIKKRTVELLPDAENN 337
>gnl|CDD|182380 PRK10328, PRK10328, DNA binding protein, nucleoid-associated;
Provisional.
Length = 134
Score = 26.8 bits (59), Expect = 9.5
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 137 TLGATSRNYSKDKTAKYIEKLKMVDFAARKSEEEQMTR 174
TL A +R +S D + +EK ++V R+ EEEQ R
Sbjct: 13 TLRAMAREFSIDVLEEMLEKFRVVT-KERREEEEQQQR 49
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the heterodimeric topo I from
Leishmania donvanni. Topo I enzymes are divided into:
topo type IA (bacterial) and type IB (eukaryotic). Topo
I relaxes superhelical tension in duplex DNA by creating
a single-strand nick, the broken strand can then rotate
around the unbroken strand to remove DNA supercoils and,
the nick is religated, liberating topo I. These enzymes
regulate the topological changes that accompany DNA
replication, transcription and other nuclear processes.
Human topo I is the target of a diverse set of
anticancer drugs including camptothecins (CPTs). CPTs
bind to the topo I-DNA complex and inhibit re-ligation
of the single-strand nick, resulting in the accumulation
of topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 27.5 bits (61), Expect = 9.9
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 148 DKTAKYIEKLKMVDFAA-------RKSEEEQMTRDEKKA 179
DK I KL++ DF K +++ T++EKKA
Sbjct: 70 DKRHHPIRKLELCDFTPIYEWHLREKEKKKSRTKEEKKA 108
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
0.312 0.125 0.352
Gapped
Lambda K H
0.267 0.0552 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,359,967
Number of extensions: 1593653
Number of successful extensions: 1406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1402
Number of HSP's successfully gapped: 59
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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: 42 (21.9 bits)
S2: 60 (27.3 bits)