RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11625
(314 letters)
>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 = 66.1 bits (162), Expect = 2e-14
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 214 QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
+ + E+RRR RIN+ +EL+SL+ KL KA+IL V +++++Q
Sbjct: 5 REAHNLRERRRRERINDAFDELRSLLPTL-----PPSKKLSKAEILRKAVDYIKSLQELL 59
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 64.4 bits (158), Expect = 1e-13
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 215 SNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQ 270
E+RRR RIN+ EL+ L+ + KL KA+IL + +++++++Q
Sbjct: 3 KAHNERERRRRDRINDAFEELRELLP------TPPNKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 58.0 bits (141), Expect = 2e-11
Identities = 17/56 (30%), Positives = 34/56 (60%), Gaps = 5/56 (8%)
Query: 218 PIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
E+RRR +IN +EL+SL+ ++ KL KA+IL + +++++++Q +
Sbjct: 1 NARERRRRRKINEAFDELRSLLPT-----LPKNKKLSKAEILRLAIEYIKSLQEEL 51
>gnl|CDD|128787 smart00511, ORANGE, Orange domain. This domain confers specificity
among members of the Hairy/E(SPL) family.
Length = 45
Score = 38.3 bits (90), Expect = 1e-04
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 286 QKFKSGFGDCAVEINRYISRLDGLDTEVC 314
F+SG+ +CA E++R++S+L G D +V
Sbjct: 1 SSFRSGYRECANEVSRFLSQLPGTDPDVR 29
>gnl|CDD|219453 pfam07527, Hairy_orange, Hairy Orange. The Orange domain is found
in the Drosophila proteins Hesr-1, Hairy, and Enhancer
of Split. The Orange domain is proposed to mediate
specific protein-protein interaction between Hairy and
Scute.
Length = 42
Score = 36.0 bits (84), Expect = 0.001
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 287 KFKSGFGDCAVEINRYISRLDGLDTEVC 314
KF++GF +C E+ R++S ++G+D +V
Sbjct: 1 KFRAGFRECLNEVARFLSSVEGVDPDVR 28
Score = 26.8 bits (60), Expect = 2.0
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 3 WNKGVKSRLLNHLNSCVSGL 22
+ V++RLL+HL SC++ L
Sbjct: 23 VDPDVRARLLSHLASCLNQL 42
>gnl|CDD|146144 pfam03356, Pox_LP_H2, Viral late protein H2. All Members of this
family show similarity to the vaccinia virus late
protein H2. This protein is often referred to by its
gene name of H2R. Members from this family all belong to
the viral taxon Poxviridae.
Length = 189
Score = 32.3 bits (74), Expect = 0.18
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 200 LIITALNTVLIWIFQS--NKPIMEKRRRARINNCLNELKSLILEAMR--KDPARHSKLEK 255
++I ++ +L W FQ+ N + E + ARI N + K L+ + D R L +
Sbjct: 36 VLILLISVLLFW-FQTSDNSVLSELAKYARIKNNIKSWKPLVESKTKIESDRGRALALGR 94
Query: 256 ADILE 260
D+ E
Sbjct: 95 DDLFE 99
>gnl|CDD|182725 PRK10781, rcsF, outer membrane lipoprotein; Reviewed.
Length = 133
Score = 31.6 bits (72), Expect = 0.23
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 75 RLPTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSP 127
LP LAL+L+G S L SP E S + E KPK+P +P
Sbjct: 3 ALPICLLALMLTGCSMLSRSPVEPVQSTAPP-------PKAEPAKPKAPRAAP 48
>gnl|CDD|173838 cd00567, ACAD, Acyl-CoA dehydrogenase. Both mitochondrial acyl-CoA
dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases
(AXO) catalyze the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of ACAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. In contrast, AXO catalyzes
a different oxidative half-reaction, in which the
reduced FAD is reoxidized by molecular oxygen. The ACAD
family includes the eukaryotic beta-oxidation enzymes,
short (SCAD), medium (MCAD), long (LCAD) and very-long
(VLCAD) chain acyl-CoA dehydrogenases. These enzymes all
share high sequence similarity, but differ in their
substrate specificities. The ACAD family also includes
amino acid catabolism enzymes such as Isovaleryl-CoA
dehydrogenase (IVD), short/branched chain acyl-CoA
dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase
(IBDH), glutaryl-CoA deydrogenase (GCD) and
Crotonobetainyl-CoA dehydrogenase. The mitochondrial
ACAD's are generally homotetramers, except for VLCAD,
which is a homodimer. Related enzymes include the SOS
adaptive reponse proten aidB, Naphthocyclinone
hydroxylase (NcnH), and and Dibenzothiophene (DBT)
desulfurization enzyme C (DszC).
Length = 327
Score = 32.6 bits (75), Expect = 0.23
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 8/48 (16%)
Query: 259 LEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAVEINRYISRL 306
L+ V++ + QR+Q +A V K D A E+ +RL
Sbjct: 209 LDEAVEYAK--QRKQFGKPLAEFQAVQFK----LADMAAEL--EAARL 248
>gnl|CDD|237782 PRK14666, uvrC, excinuclease ABC subunit C; Provisional.
Length = 694
Score = 32.2 bits (73), Expect = 0.41
Identities = 20/116 (17%), Positives = 39/116 (33%), Gaps = 17/116 (14%)
Query: 25 LTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALL 84
L F P ST PP + +P P ++ A + + ++P L
Sbjct: 297 LGQFYGPQST--IPPRIVVPWLPDTEGREGDDLAPTA---VCTDAGLLPDTPL---LPDA 348
Query: 85 LSGSSG-----LFSSPPEVSSSESSSSDRVSAFSVVEHKKP----KSPPPSPTSST 131
GSS ++P + S + + ++ + V H P + + +
Sbjct: 349 PEGSSDPVVPVAAATPVDASLPDVRTGTAPTSLANVSHADPAVAQPTQAATLAGAA 404
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 31.7 bits (72), Expect = 0.53
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 77 PTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSV-VEHKKPKSPPPSPTSSTDGDV 135
E L +S ++ S E++SS++ + S +P S SP+S DG
Sbjct: 24 DDDEDLLEVSSTTSSPVGSISWSVRETASSNKARSRSEKWNPDQPGSRVSSPSSKKDGTS 83
Query: 136 VYLSPHNAEVTSTSTTQD 153
LS ++ S ++Q
Sbjct: 84 RSLSSQVDDLASAVSSQS 101
>gnl|CDD|222970 PHA03072, PHA03072, putative viral membrane protein; Provisional.
Length = 190
Score = 30.8 bits (70), Expect = 0.61
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 200 LIITALNTVLIWIFQS--NKPIMEKRRRARINNCLNELKSLILE--AMRKDPARHSKLEK 255
+II A++ +L+W FQ+ N E + ARI N + + L+ + D R +
Sbjct: 36 VIILAISVLLLW-FQTSDNSVFSELTKYARIKNNVKSWRPLVESKTKLESDRGRLLAAGR 94
Query: 256 ADILE 260
D+ E
Sbjct: 95 DDLFE 99
>gnl|CDD|223067 PHA03380, PHA03380, transactivating tegument protein VP16;
Provisional.
Length = 432
Score = 31.2 bits (71), Expect = 0.69
Identities = 34/117 (29%), Positives = 47/117 (40%), Gaps = 16/117 (13%)
Query: 25 LTPFSLPSST-TAPPPPVTLPPA---PSLLEDVNNNEASARLQMISSGIQVIPSRLPTGE 80
S PSS A PPP PA LL ++ +E A L + + + + S LPT E
Sbjct: 28 PYATSAPSSAQLALPPPRPASPAALYQRLLTELGFSEGPALLSALETWNEDLFSCLPTNE 87
Query: 81 ----LALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDG 133
A LLS SP EV + + + S + H P P P ++ D
Sbjct: 88 DLYREAALLST------SPSEVVEAGDAPTPTRSPIDLNAHG--SEPFPEPPATEDE 136
>gnl|CDD|227785 COG5498, ACF2, Predicted glycosyl hydrolase [Cell envelope
biogenesis, outer membrane].
Length = 760
Score = 31.4 bits (71), Expect = 0.78
Identities = 19/64 (29%), Positives = 23/64 (35%), Gaps = 5/64 (7%)
Query: 71 VIPSRLPTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSS 130
VI PTG A S S S E S + + S F V+H P P P
Sbjct: 29 VIILLFPTGASASPHSVSVPKGDSNVEFPPILSGTINPPSTFRSVQH-----PVPPPGVR 83
Query: 131 TDGD 134
+D
Sbjct: 84 SDST 87
>gnl|CDD|129050 smart00814, Alpha_TIF, Alpha trans-inducing protein (Alpha-TIF).
Alpha-TIF (VP16) from Herpes Simplex virus is an
essential tegument protein involved in the
transcriptional activation of viral immediate early (IE)
promoters (alpha genes) during the lytic phase of viral
infection. VP16 associates with cellular transcription
factors to enhance transcription rates, including the
general transcription factor TFIIB and the
transcriptional coactivator PC4. The N-terminal residues
of VP16 confer specificity for the IE genes, while the
C-terminal residues are responsible for transcriptional
activation. Within the C-terminal region are two
activation regions that can independently and
cooperatively activate transcription. VP16 forms a
transcriptional regulatory complex with two cellular
proteins, the POU-domain transcription factor Oct-1 and
the cell-proliferation factor HCF-1. VP16 is an
alpha/beta protein with an unusual fold. Other
transcription factors may have a similar topology.
Length = 356
Score = 30.4 bits (69), Expect = 1.1
Identities = 32/115 (27%), Positives = 47/115 (40%), Gaps = 8/115 (6%)
Query: 26 TPFSLPSSTTAPPPPVTLPPA---PSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELA 82
P S+ A PPP PA LL ++ E A L + + + + S PT E
Sbjct: 13 APGYPSSAQLALPPPRPASPAALYQRLLTELGFAEGPALLSALETWNEDLFSCFPTNE-- 70
Query: 83 LLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVY 137
L + L +SP EV S+ +R S + H P PSP ++ + Y
Sbjct: 71 DLYREAKILSTSPSEVIEL-LSTPERTSPIDLNAHG--DEPFPSPPATEEELPAY 122
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.5 bits (69), Expect = 1.4
Identities = 26/119 (21%), Positives = 35/119 (29%), Gaps = 6/119 (5%)
Query: 18 CVSGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLP 77
C G + P P+ T P + AS+ PS
Sbjct: 247 CGWGPENECPLPRPAPITLPTRIWE--ASGWNGPSSRPGPASSSSSPRERSPSPSPSSPG 304
Query: 78 TGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSV----VEHKKPKSPPPSPTSSTD 132
+G SS SS SSS SSSS+ +V + P P P +
Sbjct: 305 SGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPS 363
Score = 28.6 bits (64), Expect = 6.2
Identities = 22/97 (22%), Positives = 31/97 (31%), Gaps = 13/97 (13%)
Query: 31 PSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSG 90
P ++ PPP T PPA S + + + S G S G
Sbjct: 109 PGPSSPDPPPPTPPPA-SPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGA---------- 157
Query: 91 LFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSP 127
S S + SS + S E + S PP+
Sbjct: 158 --SPAAVASDAASSRQAALPLSSPEETARAPSSPPAE 192
>gnl|CDD|165247 PHA02937, PHA02937, hypothetical protein; Provisional.
Length = 310
Score = 29.9 bits (67), Expect = 1.6
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 16/76 (21%)
Query: 201 IITALNTVLIWIFQSNK-------PIMEKRRRARINNCLNELKSLILEAMRKDPARHSKL 253
+ I + NK I+++ + ++NN L L ++ + +
Sbjct: 126 GYKTATLIYILVDNKNKDRINIIQKIIKENAKIKVNNALEILSTIETK---------IMI 176
Query: 254 EKADILEMTVKHLQNV 269
E + + T+K L NV
Sbjct: 177 EFRLVKDETIKMLLNV 192
>gnl|CDD|241509 cd13355, PH-GRAM_MTM1, Myotubularian 1 protein (MTM1) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTM1 is
a member of the myotubularin protein phosphatase gene
family. It is required for muscle cell differentiation
and mutations in this gene have been identified as being
responsible for X-linked myotubular myopathy, a severe
congenital muscle disorder characterized by defective
muscle cell development. Since its initial discovery,
there have been an additional 14 myotubularin-related
proteins identified. MTM1 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein can self-associate and form heteromers with
MTMR12. MTM1 contains a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, an active
PTP domain, a SET-interaction domain, and a C-terminal
coiled-coil region. Myotubularin-related proteins are a
subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. The GRAM domain, found in
myotubularins, glucosyltransferases, and other putative
membrane-associated proteins, is part of a larger motif
with a pleckstrin homology (PH) domain fold. All MTMRs
contain a N-terminal PH-GRAM domain, a Rac-induced
recruitment domain (RID) domain, a PTP domain (which may
be active or inactive), a SET-interaction domain, and a
C-terminal coiled-coil region. In addition some members
contain DENN domain N-terminal to the PH-GRAM domain and
FYVE and PH domains C-terminal to the coiled-coil
region.
Length = 152
Score = 28.9 bits (65), Expect = 2.3
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 93 SSPPEVSSSESSSSDRVSAFSVVEHKKPKSPP--PSPTSSTDGDVVYLSPHNAEV 145
S E S + +S D + + + P P TD +V+Y+ P N V
Sbjct: 1 SHNLENESIKRTSRDGLK------MELLEDVPRLPGEERITDKEVIYICPFNGPV 49
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 29.4 bits (66), Expect = 3.3
Identities = 11/43 (25%), Positives = 15/43 (34%)
Query: 92 FSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGD 134
S P S+ + V A KKP + + S D D
Sbjct: 1275 LDSAPAQSAKMEETVKAVPARRAAARKKPLASVSVISDSDDDD 1317
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 28.7 bits (65), Expect = 3.3
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 220 MEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVA 279
M+ R AR EL L L + P + KL+ ++L V+ L R+ L A A
Sbjct: 1 MQPRSIAR------ELALLSLGQIPAKPEKLEKLQLEELLLAAVRTLTQEVRETLDTAAA 54
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 28.4 bits (64), Expect = 3.5
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 209 LIWIFQSNKPIMEKRRRARINNCLNELKSLILE 241
LIW+ S+ RAR+ +C EL+ L++E
Sbjct: 85 LIWVVDSSD-------RARLEDCKRELQKLLVE 110
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 28.9 bits (64), Expect = 4.7
Identities = 38/140 (27%), Positives = 50/140 (35%), Gaps = 21/140 (15%)
Query: 24 QLTPFSLPSSTTAPPPPV-----TLPP-----APSLLEDVNNNEASARLQMISSGIQVI- 72
QL P S P + PPV +LPP S L A+ S G+ I
Sbjct: 407 QLMPQSQPLQSVPAQPPVLTQSQSLPPKASTHPHSGLHSGPPQSPFAQHPFTSGGLPAIG 466
Query: 73 -PSRLPTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVV--------EHKKPKSP 123
P LPT A SSG P S + + E ++P+SP
Sbjct: 467 PPPSLPTSTPAAPPRASSGS-QPPGSALPSSGGCAGPGPPLPPIQIKEEPLDEAEEPESP 525
Query: 124 PPSPTSSTDGDVVYLSPHNA 143
PP P S + V +P +A
Sbjct: 526 PPPPRSPSPEPTVVNTPSHA 545
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor,
cyanobacterial RpoD-like family. This family includes a
number of closely related sigma-70 (TIGR02937) factors
in the cyanobacteria. All appear most closely related to
the essential sigma-70 factor RpoD, and some score above
trusted to the RpoD C-terminal domain model (TIGR02393).
Length = 298
Score = 28.4 bits (64), Expect = 5.0
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 211 WIFQS-NKPIMEKRRRAR----INNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKH 265
WI Q + I + R R I LN++K + E +K S+ E A+ LE+ +
Sbjct: 134 WIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQ 193
Query: 266 LQNVQRQ 272
++ + ++
Sbjct: 194 VRELLQR 200
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 28.4 bits (63), Expect = 5.5
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 86 SGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVYLSPHNAEV 145
+ FSSP + S S+S + V+ K+ +S + +S SP N E+
Sbjct: 134 LTNISFFSSPTSIYSCLSNSLSSKHSPKVI--KENQSTHVNISSDN-------SPRNKEI 184
Query: 146 TSTS 149
++
Sbjct: 185 SNKQ 188
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 28.7 bits (64), Expect = 5.5
Identities = 36/177 (20%), Positives = 60/177 (33%), Gaps = 11/177 (6%)
Query: 30 LPSSTTAPPPPVTLPPAPSL---LEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLS 86
L + P P A S L + ++ S +S SR +G
Sbjct: 82 LFQRRNSAGPITHSPSATSSTSSLNSNDGDQFSPASDSLSFNPSSTQSRKDSGPGDGSPV 141
Query: 87 GSSGLFSSP--PEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVYL-SPHNA 143
+P P S+ + + + P + S + L SPH
Sbjct: 142 QKR---KNPLLPSSSTHGTHPPIVFTDNNGSHAGAPNARSRKEIPSLGSQSMQLPSPHFR 198
Query: 144 EVTSTSTTQDNVFKVPSLQTKAF-SSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSI 199
+ S+S T N F PS++ + SS P+++ + LL + A SS+I
Sbjct: 199 QKFSSSDTS-NGFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSGASLISSNI 254
>gnl|CDD|233528 TIGR01684, viral_ppase, viral phosphatase. This model represents a
family of viral proteins of unknown function. These
proteins are members, however, of the IIIC (TIGR01681)
subfamily of the haloacid dehalogenase (HAD) superfamily
of aspartate nucleophile hydrolases. All characterized
members of the III subfamilies (IIIA, TIGR01662; IIIB,
pfam03767) are phosphatases, including MDP-1, a member
of subfamily IIIC (TIGR01681). No member of this
subfamily is characterized with respect to particular
function. All of the active site residues characteristic
of HAD-superfamily phosphatases are present in subfamily
IIIC. These proteins also include an N-terminal domain
(ca. 125 aas) that is unique to this clade.
Length = 301
Score = 28.2 bits (63), Expect = 5.6
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 134 DVVYLSPHNAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVP 187
D++ H AE ST +T+D ++ F+ P Y + T + L K P
Sbjct: 190 DIIISGGHKAEEYSTMSTEDRQYR------YVFTKTPFYLN--TTDGKRLPKSP 235
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 28.6 bits (63), Expect = 5.7
Identities = 38/194 (19%), Positives = 73/194 (37%), Gaps = 21/194 (10%)
Query: 33 STTAPPPPVTLPPAPSLLEDVN----NNEASARLQMISS----GIQVIPSRLPTGELALL 84
++T P + L AP + N +A + S Q++ S +PTG ++L
Sbjct: 1140 NSTPQSPVLALLLAPYISYKFNALSLGFSITADAAIFSLFGIPAPQLLSSYIPTG--SVL 1197
Query: 85 LSGSSGLFSSPPEVSSSESS------SSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVYL 138
+ P + S ++ + ++SA S +PPPS +SS+ +
Sbjct: 1198 YQDPIFTYIPPGIIGMSGTNTFTFKAAQLQLSAASSPPAATTPTPPPSSSSSSSAQSIST 1257
Query: 139 SPHNAEV--TSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKV-PPYHQAEPC 195
SP ++ ++T N P+L T P N S + + +
Sbjct: 1258 SPGQIQIVLNGSTTIHINFLFFPALSTPKIGQ--ILAMPIVNSSGAFISLYVNSAISANF 1315
Query: 196 SSSILIITALNTVL 209
+ +I + + TV+
Sbjct: 1316 NVTIEYVFSNGTVI 1329
>gnl|CDD|178778 PLN03240, PLN03240, putative Low-temperature-induced protein;
Provisional.
Length = 626
Score = 28.6 bits (63), Expect = 5.7
Identities = 16/58 (27%), Positives = 22/58 (37%)
Query: 96 PEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVVYLSPHNAEVTSTSTTQD 153
P VSSS + S+ + P P L+PHN V+ S T+D
Sbjct: 115 PVVSSSHTKHSEPIRGVGHEAMSHPIKHSGVPDKEERRGAATLTPHNTPVSLLSATED 172
>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex
that regulates RNA polymerase II activity. Med23 is
required for heat-shock-specific gene expression, and
has been shown to mediate transcriptional activation of
E1A in mice.
Length = 1341
Score = 28.3 bits (63), Expect = 6.9
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 11/66 (16%)
Query: 18 CVSGLQ---QLTPFSLPSSTTAPPPPVTL--------PPAPSLLEDVNNNEASARLQMIS 66
C L Q TP P T + PP P P+ + E R ++
Sbjct: 737 CKDFLANIMQNTPHGWPEHTLSCFPPWLNEYFKQHNVPKEPNQALKKSVEEEYRRWNSMT 796
Query: 67 SGIQVI 72
+ +I
Sbjct: 797 NENDII 802
>gnl|CDD|118692 pfam10164, DUF2367, Uncharacterized conserved protein (DUF2367).
This is a highly conserved family of proteins which
contains three pairs of cysteine residues within a
length of 42 amino acids and is rich in proline
residues towards the N-terminus. The function is
unknown. Several members are putatively assigned as
brain protein i3 but this was not validated.
Length = 98
Score = 26.4 bits (58), Expect = 7.1
Identities = 9/44 (20%), Positives = 19/44 (43%)
Query: 29 SLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVI 72
++ ++ PP P+ + P P V N + + + I V+
Sbjct: 6 AMDTAPPKPPVPIVVQPIPPSHPRVYNIHSRTVTRYPINSIIVV 49
>gnl|CDD|212062 cd11493, SLC5sbd_NIS-like_u1, uncharacterized subgroup of the
Na(+)/iodide (NIS) cotransporter subfamily; putative
solute-binding domain. Proteins belonging to the same
subfamily as this uncharacterized subgroup include i)
NIS, which transports I-, and other anions including
ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin,
pantothenic acid and lipoate, and iii) the
Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1
is a high-affinity transporter while SMCT2 is a
low-affinity transporter. This subgroup belongs to the
solute carrier 5 (SLC5) transporter family.
Length = 479
Score = 27.9 bits (63), Expect = 7.3
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 8/65 (12%)
Query: 55 NNEASARLQMISSGIQVIPSRLPTGELALLLSGSSGL--FSSPPEVSSSESSSSDRVSAF 112
N A+ +I SG+ V P + AL L L + +S+ D V +
Sbjct: 261 RNLRDAQKALIGSGVVVFP------QFALFLLIGVLLYVYYQGASLSALGLGEPDEVFPY 314
Query: 113 SVVEH 117
+V
Sbjct: 315 FIVHE 319
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.4 bits (63), Expect = 7.3
Identities = 27/136 (19%), Positives = 43/136 (31%), Gaps = 10/136 (7%)
Query: 24 QLTPFSLPSSTTAPPPPVTLP-PAPSLLEDVNNNEASARLQ--MISSGIQVIPSRLPTGE 80
P LP T AP PP P PA + + + + +V R
Sbjct: 2611 PAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL 2670
Query: 81 LALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVE-HKKPKSPPPSPTSSTDGDVVYLS 139
G + SSPP+ ++ S S+ + P +P P+P + +
Sbjct: 2671 ------GRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPG 2724
Query: 140 PHNAEVTSTSTTQDNV 155
P A S +
Sbjct: 2725 PAAARQASPALPAAPA 2740
>gnl|CDD|236644 PRK10049, pgaA, outer membrane protein PgaA; Provisional.
Length = 765
Score = 27.8 bits (62), Expect = 9.7
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 7/31 (22%)
Query: 84 LLSGSSGLFSSP-------PEVSSSESSSSD 107
LSG L+SSP P + S++S D
Sbjct: 638 SLSGQERLWSSPYLIVDFLPSLYYSQNSEHD 668
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 0.127 0.359
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,257,682
Number of extensions: 1388527
Number of successful extensions: 1552
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1508
Number of HSP's successfully gapped: 92
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
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: 59 (26.6 bits)