RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11481
(561 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 66.3 bits (163), Expect = 5e-14
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLR 237
R+ HN+ E+ RR + + FE L+ +P KK S IL AI YI+ L+
Sbjct: 2 RKAHNERERRRRDRINDAFEELRELLPTPP-NKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 64.9 bits (159), Expect = 2e-13
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 186 REVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLRRRER 241
RE HN E+ RR + + F+ L+ +P KK S IL A+ YI+ L+ +
Sbjct: 5 REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 63.4 bits (155), Expect = 5e-13
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 190 NKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLRRRERE 242
N E+ RR + E F+ L+ +P + KK S IL AI YI+ L+ ++
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|224273 COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family)
[Replication, recombination, and repair].
Length = 248
Score = 38.5 bits (90), Expect = 0.006
Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 8/102 (7%)
Query: 194 KNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIR-------YIQFLRRREREFEHE 246
K L E E + + E K I Y + LRR ++E E
Sbjct: 105 KEAAELLAELEEERRDVFSKIKPEIKIKKERRPVEEISLIDLFRAYQKILRRVKQEELVE 164
Query: 247 MERLAREKIHAQQRLALLKKELSARWEHIDFNTLIPDNMEVD 288
+ER+ E++ +++L L L A + F+ L D
Sbjct: 165 IERIVLEELSVEEQLEELLARLEA-RGVLRFSDLFSPEERKD 205
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 38.2 bits (89), Expect = 0.013
Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 11/100 (11%)
Query: 177 KKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFL 236
+ +S + E L + LKE +++ QEE++ L A L
Sbjct: 189 ELEGQLSELLEDIEDLLEALEEELKE-----LKKLEEIQEEQEEEELEQEIEA------L 237
Query: 237 RRREREFEHEMERLAREKIHAQQRLALLKKELSARWEHID 276
R E E E ERL K + +L + L R E +
Sbjct: 238 EERLAELEEEKERLEELKARLLEIESLELEALKIREEELR 277
Score = 29.0 bits (65), Expect = 8.5
Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 10/99 (10%)
Query: 170 LTQNDMIKKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSA 229
L + +++ E+ ++E L E E +R EE K+ L I
Sbjct: 212 LKELKKLEEIQEEQEEEELEQEIEALEER-LAELEEEKERL-----EELKARLLEIESLE 265
Query: 230 IRYIQFLRRREREFEHEMERLAREKIHAQQRLALLKKEL 268
+ ++ RE E +E L + +RL L++E+
Sbjct: 266 LEALKIREEELRELERLLEELEEKI----ERLEELEREI 300
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 36.4 bits (85), Expect = 0.035
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 8/89 (8%)
Query: 191 KLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLR---RREREFEHEM 247
K EK ++ +E E + ++ +EEK+ L + +++ R RE E E E
Sbjct: 119 KREKQKKL-REEIDEFNEERIERKEEEKEREREEEL----KILEYQREKAEREEEREAER 173
Query: 248 ERLAREKIHAQQRLALLKKELSARWEHID 276
EK RL ++E E +D
Sbjct: 174 RERKEEKEREVARLRAQQEEAEDEREELD 202
Score = 34.1 bits (79), Expect = 0.17
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 21/87 (24%)
Query: 185 IREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLRRREREFE 244
+RE++ KL R A + Q+ EEKK I+ + + ER +
Sbjct: 6 LRELNEKL---RAAK---VNKERDAQI----EEKK---------RIKAEE--KEEERRID 44
Query: 245 HEMERLAREKIHAQQRLALLKKELSAR 271
ME + + ++ +KE
Sbjct: 45 EMMEEERLKALAEEEERERKRKEERRE 71
>gnl|CDD|197361 cd09803, UBAN, polyubiquitin binding domain of NEMO and related
proteins. NEMO (NF-kappaB essential modulator) is a
regulatory subunit of the kinase complex IKK, which is
involved in the activation of NF-kappaB via
phosporylation of inhibitory IkappaBs. This mechanism
requires the binding of NEMO to ubiquinated substrates.
Binding is achieved via the UBAN motif (ubiquitin
binding in ABIN and NEMO), which is described in this
model. This region of NEMO has also been named CoZi (for
coiled-coil 2 and leucine zipper). ABINs (A20-binding
inhibitors of NF-kappaB) are sensors for ubiquitin that
are involved in regulation of apoptosis, ABIN-1 is
presumed to inhibit signalling via the NF-kappaB route.
The UBAN motif is also found in optineurin, the product
of a gene associated with glaucoma, which has been
characterized as a negative regulator of NF-kappaB as
well.
Length = 87
Score = 31.9 bits (73), Expect = 0.16
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 240 EREFEHEMERLAREKIHA-----QQRLALLKKELS 269
+ +FE ER AREK+H ++L L++E
Sbjct: 52 KSDFE--AERAAREKLHQEKEQLAEQLEYLQRENQ 84
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 30.3 bits (69), Expect = 0.25
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 237 RRREREFEHEMERLAREKIHAQQRLALLKKE 267
++RE E E ++ L E +Q++ L+KE
Sbjct: 24 KQREEELEERVKELEEENAQLRQKVEQLEKE 54
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 31.8 bits (73), Expect = 0.27
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 185 IREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLRRREREFE 244
+ EV L+ +R + E+LK++ +EE + + S I++ +FL+ E +
Sbjct: 9 MEEVQLALD-AKREEFERREELLKQR----EEELEKKEEELQESLIKFDKFLKENEAKRR 63
Query: 245 HEMERLAREKIHAQQR---LALLKKELSA 270
++ EK +++ + LK EL
Sbjct: 64 RAEKKAEEEKKLRKEKEEEIKELKAELEE 92
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 33.5 bits (77), Expect = 0.36
Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 6/90 (6%)
Query: 173 NDMIKKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRY 232
+ ++ ++G+R +LEK RR +K+ E LK ++ + EK L L A+
Sbjct: 666 EEYLELSRELAGLRAELEELEK-RREEIKKTLEKLKEEL--EEREKAKKELEKLEKALER 722
Query: 233 IQFLRRREREFEHEMERLAREKIHAQQRLA 262
++ LR + ++++ ++ A K+ +A
Sbjct: 723 VEELREKVKKYKALLKERALSKV---GEIA 749
Score = 28.9 bits (65), Expect = 9.5
Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 15/98 (15%)
Query: 175 MIKKRSGISGIREVHNKLEKNRRAHLK---ECFEILKRQVPPAQEEKKSSNLSILHSAIR 231
+IK + ++E+ KL+K L+ E +E LK ++ K + L +
Sbjct: 495 LIKLKELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKL-----IKLKGEIKSLKKELE 549
Query: 232 YIQFLRRREREFEHEMERLAREKIHAQQRLALLKKELS 269
++ L+++ E E +++ L E LA L KEL
Sbjct: 550 KLEELKKKLAELEKKLDELEEE-------LAELLKELE 580
>gnl|CDD|111851 pfam03007, WES_acyltransf, Wax ester synthase-like Acyl-CoA
acyltransferase domain. This domain is found in wax
ester synthase genes. In these proteins this domain
catalyzes the CoA dependent acyltransferase reaction
with fatty alcohols to form wax esters.
Length = 263
Score = 32.7 bits (75), Expect = 0.42
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 16 KPSSCYTNGVSGSNLGSVITTLSPDPAAHPLSH 48
K +GV G NL + + L PDP P
Sbjct: 134 KVHHALADGVGGLNLLARLLDLDPDPPPRPTPP 166
>gnl|CDD|238416 cd00801, INT_P4, Bacteriophage P4 integrase. P4-like integrases are
found in temperate bacteriophages, integrative plasmids,
pathogenicity and symbiosis islands, and other mobile
genetic elements. They share the same fold in their
catalytic domain and the overall reaction mechanism with
the superfamily of DNA breaking-rejoining enzymes. The
P4 integrase mediates integrative and excisive
site-specific recombination between two sites, called
attachment sites, located on the phage genome and the
bacterial chromosome. The phage attachment site is often
found adjacent to the integrase gene, while the host
attachment sites are typically situated near tRNA genes.
Length = 357
Score = 32.6 bits (75), Expect = 0.58
Identities = 19/66 (28%), Positives = 22/66 (33%), Gaps = 18/66 (27%)
Query: 235 FLRRRE-REFEHEMERLAREKIHAQQRLALL--------KKELS-ARWEHIDFNTLIPDN 284
L E EF ++ L RLAL EL ARW ID +N
Sbjct: 179 ALSPDELPEF---LQALDAASGSPVTRLALKLLLLTGVRPGELRGARWSEIDL-----EN 230
Query: 285 MEVDIP 290
IP
Sbjct: 231 ALWTIP 236
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 31.7 bits (72), Expect = 1.3
Identities = 24/126 (19%), Positives = 42/126 (33%), Gaps = 6/126 (4%)
Query: 162 ALSTSPNNLTQNDMIKKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSS 221
AL T + I LE+ +E + L R + + + +
Sbjct: 385 ALPTVTVPEPLRAALADALRAGDIDAALAALEQEVAVAKRELAQALSR-LGLWRGDLEEL 443
Query: 222 NLSILHSAIRYIQFLRRREREFEHEMERLAREKIHAQQRLALLKKELSARWEHIDFNTLI 281
+ SA + FL+ E E+ + R+K L + L + H+D +
Sbjct: 444 VALPVPSAEQVQAFLKEAE-----EIMQAKRQKRDRLLELEEDLETLELQLRHLDAAGAV 498
Query: 282 PDNMEV 287
P EV
Sbjct: 499 PTEEEV 504
>gnl|CDD|149040 pfam07756, DUF1612, Protein of unknown function (DUF1612). This
family includes sequences of largely unknown function
but which share a number of features in common. They are
expressed by bacterial species, and in many cases these
bacteria are known to associate symbiotically with
plants. Moreover, the majority are coded for by
plasmids, which in many cases are known to confer on the
organism the ability to interact symbiotically with
leguminous plants. An example of such a plasmid is
NGR234, which encodes Y4CF, a protein of unknown
function that is a member of this family. Other members
of this family are expressed by organisms with a
documented genomic similarity to plant symbionts.
Length = 129
Score = 30.0 bits (68), Expect = 1.5
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 215 QEEKKSSNLSILHSAIRYIQFLRRREREFE-------HEMERLAREKIHAQQRLALLKKE 267
Q K +S+L L+ ++ I RRR R E +E A + RL+L +++
Sbjct: 63 QRGKTASHLPALNLGLKTIPRERRRHRNRETRLLAFLEAIEAAAEAGLKEHDRLSLAREQ 122
Query: 268 LSAR 271
+ +
Sbjct: 123 MERK 126
>gnl|CDD|150747 pfam10107, Endonuc_Holl, Endonuclease related to archaeal Holliday
junction resolvase. This domain is found in various
predicted bacterial endonucleases which are distantly
related to archaeal Holliday junction resolvases.
Length = 153
Score = 30.0 bits (68), Expect = 1.9
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 223 LSILHSAIRYIQ----FLRRREREFE----HEMERLAREKIHAQQRLALLKKELSAR 271
L+IL I+ I+ +R FE E E A + A+ K+E R
Sbjct: 4 LAILSLFIKIIKLQGKVEKRARELFEQWRNAEREAQAMREAEAKFEEWQKKEEKEIR 60
>gnl|CDD|225518 COG2971, COG2971, Predicted N-acetylglucosamine kinase
[Carbohydrate transport and metabolism].
Length = 301
Score = 30.3 bits (69), Expect = 2.5
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 311 DEDGGLVIVTNGSVGLERSDGGESGSSLGGGGEMISGRGEGEY-GRAG 357
D+DG +VI GS+G R GG +GG G I G G + GR
Sbjct: 116 DDDGIIVIAGTGSIGYGR-KGGRR-ERVGGWGFPIGDEGSGAWIGREA 161
>gnl|CDD|220366 pfam09728, Taxilin, Myosin-like coiled-coil protein. Taxilin
contains an extraordinarily long coiled-coil domain in
its C-terminal half and is ubiquitously expressed. It is
a novel binding partner of several syntaxin family
members and is possibly involved in Ca2+-dependent
exocytosis in neuroendocrine cells. Gamma-taxilin,
described as leucine zipper protein Factor Inhibiting
ATF4-mediated Transcription (FIAT), localises to the
nucleus in osteoblasts and dimerises with ATF4 to form
inactive dimers, thus inhibiting ATF4-mediated
transcription.
Length = 309
Score = 30.4 bits (69), Expect = 2.6
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 215 QEEKK-----SSNLSILHSAIRYIQFLRRREREFEHEMERLAREKIHAQQRLALLKKE 267
+E KK + +LS L + ++ L +R E EM+RL ++ Q+R L+KE
Sbjct: 1 KEVKKAARLLNQSLSKLDTPEEKLETLIKRLAELLKEMKRLEKDLKKLQKRGEQLQKE 58
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.4 bits (69), Expect = 3.1
Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 183 SGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAI-RYIQFLRRRER 241
+ ++E+ KLE+ R + L+ ++ Q+E L+ S + + Q LR R
Sbjct: 260 AELQELEEKLEELRLEVSE-----LEEEIEELQKELY--ALANEISRLEQQKQILRERLA 312
Query: 242 EFEHEMERLAREKIHAQQRLALLKKELSARWE 273
E ++E L + + +L L +EL A E
Sbjct: 313 NLERQLEELEAQLEELESKLDELAEEL-AELE 343
>gnl|CDD|236733 PRK10672, PRK10672, rare lipoprotein A; Provisional.
Length = 361
Score = 29.6 bits (67), Expect = 4.1
Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 13/93 (13%)
Query: 356 AGSSSGASNLLKCSESTLYSSNSSLSSTMSPLHNQTHIQLPYRPTQSTCPSVIQSSVINT 415
+ + ++L S STL S T +P+ + + P+ + V+
Sbjct: 210 QPAPAPQGDVLPVSNSTL----KSEDPTGAPVTSSGFL---------GAPTTLAPGVLEG 256
Query: 416 LSASNGVPASAGYNGKPATSPAMVPATPVSTNG 448
+ P+SA A +P + ++
Sbjct: 257 SEPTPTAPSSAPATAPAAAAPQAAATSSSASGN 289
>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 29.9 bits (68), Expect = 4.2
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 2/79 (2%)
Query: 194 KNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRY--IQFLRRREREFEHEMERLA 251
++ L+ L+ + P ++ L L +R L +++ E +RL
Sbjct: 286 DQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRLRRALENQLALKKQRLERLTQRLN 345
Query: 252 REKIHAQQRLALLKKELSA 270
+ QQRL L++ L
Sbjct: 346 PQIQRQQQRLQQLERRLDK 364
>gnl|CDD|193185 pfam12709, Kinetocho_Slk19, Central kinetochore-associated. This
is a family of proteins integrally involved in the
central kinetochore. Slk19 is a yeast member and it may
play an important role in the timing of nuclear
migration. It may also participate, directly or
indirectly, in the maintenance of centromeric tensile
strength during mitotic stagnation, for instance during
activation of checkpoint controls, when cells need to
preserve nuclear integrity until cell cycle progression
can be resumed.
Length = 87
Score = 27.7 bits (62), Expect = 4.3
Identities = 12/65 (18%), Positives = 30/65 (46%), Gaps = 13/65 (20%)
Query: 236 LRRREREFEHEMERLAREKIHAQ------QRLALLKKELSARWE------HIDFNTLIPD 283
L +E+E ++ LA + ++ Q Q++ +LKK A+++ ++ L +
Sbjct: 6 LEEKEQETNKRLQLLAED-LYVQYSSKHEQKVKMLKKGYEAKYQKKLDELELENKALKQE 64
Query: 284 NMEVD 288
++
Sbjct: 65 IEQLK 69
>gnl|CDD|153384 cd07372, 2A5CPDO_B, The beta subunit of the Class III extradiol
dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase,
which catalyzes the oxidization and subsequent
ring-opening of 2-amino-5-chlorophenol.
2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO),
catalyzes the oxidization and subsequent ring-opening of
2-amino-5-chlorophenol, which is an intermediate during
p-chloronitrobenzene degradation. This enzyme is a
member of the class III extradiol dioxygenase family, a
group of enzymes which use a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. The active 2A5CPDO
enzyme is probably a heterotetramer, composed of two
alpha and two beta subunits. The alpha and beta subunits
share significant sequence similarity and may have
evolved by gene duplication. This model describes the
beta subunit, which contains a putative metal binding
site with two conserved histidines; these residues are
equivalent to two out of three Fe(II) binding residues
present in the catalytic subunit dioxygenase LigB. The
alpha subunit does not contain these potential metal
binding residues. The 2A5CPDO beta subunit may be the
catalytic subunit of the enzyme.
Length = 294
Score = 29.6 bits (66), Expect = 4.5
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 192 LEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRY 232
+E R+ +KE F +L + + A E KS + +H+A++Y
Sbjct: 224 IELMRQGRMKEVFRLLPQFIEEAFAEVKSGAFTWMHAAMQY 264
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 27.9 bits (63), Expect = 4.7
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 234 QFLRRREREFEHEMERLAREKIHAQQRLALL 264
+ LR + E E E+E L R + RL +
Sbjct: 78 KLLREKLAELEAEIEELQRILRLLEDRLKQI 108
>gnl|CDD|148617 pfam07111, HCR, Alpha helical coiled-coil rod protein (HCR). This
family consists of several mammalian alpha helical
coiled-coil rod HCR proteins. The function of HCR is
unknown but it has been implicated in psoriasis in
humans and is thought to affect keratinocyte
proliferation.
Length = 739
Score = 29.6 bits (66), Expect = 4.8
Identities = 34/142 (23%), Positives = 58/142 (40%), Gaps = 17/142 (11%)
Query: 128 IEDEMMGSREVVASLSGETRLVAHNNYTSNSHAVALSTSPNNLTQNDMIKKRSGISGIRE 187
+E E+ S+E +AS + S A +L LTQ + ++ + E
Sbjct: 526 LERELQESQESLASAGAQLEAARAGQQESTEEAASLR---QELTQQQEVYGQALQEKVAE 582
Query: 188 VHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRYIQFLRRREREFEHEM 247
V L+E +R++ A+ E + +S+ R IQ +E+E E+
Sbjct: 583 VE--------TRLREQLSDTERRLNEARREHAKAVVSL-----RQIQRQAAQEKERNQEL 629
Query: 248 ERLAREKIHAQ-QRLALLKKEL 268
RL E + QRL+ +EL
Sbjct: 630 RRLQEEARKEEGQRLSRRLQEL 651
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast
subunit 62; Provisional.
Length = 576
Score = 29.5 bits (66), Expect = 5.3
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 431 KPATSPAMVPATPVSTNGMSTATIIKSGDSIPAN 464
KP TSP+ T VS + ST+++ D+ PA
Sbjct: 448 KPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPAT 481
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.4 bits (66), Expect = 5.5
Identities = 11/103 (10%), Positives = 24/103 (23%)
Query: 449 MSTATIIKSGDSIPANVTPKLVSLNSLPGLVSAHHSAQVLFTSSQHPKMLSSTSVVTSPP 508
+ A + + GD PK +A + S + ++
Sbjct: 357 IQLAQLTQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQS 416
Query: 509 VIKPLPSLQPISSHQIILKPSLAQVNGAPRLVLPHHSAPVTMP 551
+P + +S P + +P
Sbjct: 417 ATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIP 459
>gnl|CDD|233945 TIGR02597, TIGR02597, TIGR02597 family protein. This model
describes a paralogous family with at least ten members
in Verrucomicrobium spinosum. Two additional predicted
proteins match more weakly and score between the trusted
and noise cutoffs, while a third contains a point
mutation. Eleven of the thirteen genes are found in a
single tandem array.
Length = 361
Score = 29.4 bits (66), Expect = 5.6
Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 385 SPLHNQTHIQLPY-RPT--QSTCPSVIQSSVINTLSASNGVPASAGYNG--KPATSPAMV 439
+P ++ T + P+ RP + T SV + V+ L N Y +P V
Sbjct: 25 APGNSDTRVSAPFHRPPEFRGTVTSVSGNGVVTVLGTPNWASNQFVYAAGTQPNHFYVRV 84
Query: 440 PAT-------PVSTNGMSTATIIKSGDSIPANVTP 467
+ ++ N +T TI SGD+I V P
Sbjct: 85 TSGSRAGMYYTITANTTATLTIDLSGDNIDGGVQP 119
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.3 bits (66), Expect = 6.4
Identities = 16/96 (16%), Positives = 34/96 (35%), Gaps = 5/96 (5%)
Query: 173 NDMIKKRSGISGIREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNLSILHSAIRY 232
+ + + I + ++ A ++ EI K QEE+K L
Sbjct: 691 SSLQSELRRIE--NRLDELSQELSDAS-RKIGEIEKEIEQLEQEEEKLK--ERLEELEED 745
Query: 233 IQFLRRREREFEHEMERLAREKIHAQQRLALLKKEL 268
+ L + + E++ L ++ L L++ L
Sbjct: 746 LSSLEQEIENVKSELKELEARIEELEEDLHKLEEAL 781
>gnl|CDD|129409 TIGR00309, V_ATPase_subD, H(+)-transporting ATP synthase, vacuolar
type, subunit D. Although this ATPase can run
backwards, using a proton gradient to synthesize ATP,
the primary biological role is to acidify some
compartment, such as yeast vacuole (a lysosomal homolog)
or the interior of a prokaryote [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 209
Score = 28.6 bits (64), Expect = 6.8
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 169 NLTQNDMIKKRSGISGIREVHNKLEKNRRAHLKECFEILKR--QVPPAQEEKKSSNLSIL 226
N T+ +++K + + + ++ L+ R A + E +IL+R + E+K +S L
Sbjct: 5 NPTRMELLKLKDKLKMAKRGYSLLKLKRDALIMEFRQILERAKDIKNKMEQKLKEAISDL 64
Query: 227 HSAIR-------YIQFLRRREREFEHEMERL 250
A +I L FE +M+
Sbjct: 65 IEAQSVMGPFAVWIAALSVVTARFEVDMKSK 95
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.1 bits (66), Expect = 6.8
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 13/54 (24%)
Query: 233 IQFLRRREREFEHEMERLAREKIHA---QQRLALLKKELSA----------RWE 273
++ LRRR E E++ L RE +RLA L+ EL+A RW+
Sbjct: 421 LEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQ 474
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 28.9 bits (65), Expect = 6.9
Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 320 TNGSVGLERSDGGESGSSLGGGGEMISGR--GEGEYGRAGSSS 360
NG +G R G GS GGG G G G G G+S
Sbjct: 227 LNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG 269
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 28.9 bits (65), Expect = 7.9
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 185 IREVHNKLEKNRRAHLKECFEILKRQVPPAQEEKKSSNL-SILHSAIRYIQFLRRREREF 243
I+++ +E+ L+E LKR++ + +++ L S L R ++ R++RE
Sbjct: 424 IKKLEETVER-----LEEENSELKREL--EELKREIEKLESELERFRREVRDKVRKDREI 476
Query: 244 EH---EMERLAREKIHAQQRLALLKKEL 268
+ERL +E ++R+ L+++L
Sbjct: 477 RARDRRIERLEKELEEKKKRVEELERKL 504
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 29.2 bits (66), Expect = 8.4
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 236 LRRREREFEHEMERLAREKIHA-QQRLALLKKE----------LSARWE 273
L RR + E E E L +EK A ++RL L+KE L +W+
Sbjct: 410 LDRRIIQLEIEREALKKEKDEASKERLEDLEKELAELEEEYADLEEQWK 458
>gnl|CDD|215191 PLN02333, PLN02333, glucose-6-phosphate 1-dehydrogenase.
Length = 604
Score = 28.8 bits (64), Expect = 8.7
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 221 SNLSILHSAIRYIQFLRRREREFEHEMERLAREKIHAQQRLALLKKELSARW 272
SNL++L++A R +E ERL + I ++RL + EL A W
Sbjct: 513 SNLNLLYAA--------RYSKEIPDAYERLLLDAIEGERRLFIRSDELDAAW 556
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.1 bits (66), Expect = 8.8
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 202 ECFEILKRQVPPAQEEK---KSSNLSILHSAIRYIQFLRRRE---REFEHEMERLAR 252
E EI KR + P Q ++ K L+I AI+ I RE R E E+ ++ R
Sbjct: 499 EKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYYTREAGVRNLEREIAKICR 555
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 29.0 bits (64), Expect = 9.4
Identities = 35/164 (21%), Positives = 48/164 (29%), Gaps = 19/164 (11%)
Query: 369 SESTLYSSNSSLSSTMSPLHNQTHIQLPYRPTQSTCPSVIQSSVINTLSASNGVPASAGY 428
+ STL S S T S N T +T P+ ++S
Sbjct: 478 TSSTLPEDTSPTSRTTSATPNATSPTPAVTTPNATSPTTQKTS-----------DTPNAT 526
Query: 429 NGKPA--TSPAMVPATPVSTNGMSTATIIKSGDSIPANVTPKLVSLNSLPGLVSAHHSAQ 486
+ P + P T + AT + + P N T V ++ L SA + Q
Sbjct: 527 SPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPVNNTNTPVVTSAPSVLTSAVTTGQ 586
Query: 487 VLFTSSQ------HPKMLSSTSVVTSPPVIKPLPSLQPISSHQI 524
SS P ST S L S P I
Sbjct: 587 HGTGSSPTSQQPGIPSSSHSTPRSNSTSTTPLLTSAHPTGGENI 630
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 28.8 bits (64), Expect = 9.8
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 7/84 (8%)
Query: 24 GVSGSNLGSVITTLSPDPAAH---PLS----HLHHSLPTTTIINTTNHITFTNGLPSSLL 76
G++ + L I S P+ + PLS S + + N + +S
Sbjct: 50 GIAIATLVFTIFPSSSQPSPYSVDPLSGYGIRPDESYVPAIQAQRKPSLEYLNRIGNSGG 109
Query: 77 HRPLERKEELLLTTTSNGAHFVES 100
PL K + L + GA FV S
Sbjct: 110 KIPLGLKRKGLRVVVTGGAGFVGS 133
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
0.311 0.126 0.353
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,551,015
Number of extensions: 2637161
Number of successful extensions: 2216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2197
Number of HSP's successfully gapped: 76
Length of query: 561
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 459
Effective length of database: 6,413,494
Effective search space: 2943793746
Effective search space used: 2943793746
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 (21.8 bits)
S2: 62 (27.6 bits)