RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5860
(138 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 72.1 bits (178), Expect = 4e-18
Identities = 27/52 (51%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 25 RRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYL 76
RR N++ERRR IN+AF +LRE +P P + KLSK + LRLA YI +L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHL 51
>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 = 69.2 bits (170), Expect = 8e-17
Identities = 26/59 (44%), Positives = 36/59 (61%)
Query: 23 VKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILE 81
RR N +ERRR + IN+AF +LR +P +P KLSK + LR A YI L ++L+
Sbjct: 2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 66.9 bits (164), Expect = 5e-16
Identities = 25/53 (47%), Positives = 34/53 (64%)
Query: 30 NKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET 82
N +ERRR + IN AF +LR +P +P + KLSK + LRLA YI L + L+
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 30.3 bits (69), Expect = 0.27
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 56 SDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKAD 94
S+ KLSK + RLA L+ + E DI+ +D++ AD
Sbjct: 446 SNLKLSKGQKKRLA-----LLLALAEERDILLLDEWAAD 479
>gnl|CDD|205352 pfam13171, DUF4004, Protein of unknown function (DUF4004). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 210 amino acids in length.
Length = 199
Score = 28.8 bits (65), Expect = 0.79
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 2/63 (3%)
Query: 78 KILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMD--PSCQQYTSPA 135
KI + D +S+D+ S + + + I S + + + + +
Sbjct: 58 KIQKMKDDLSLDELAKMFSPNMEEVELTEEELLRKGIVSETALEVFEEIVGKAEVFEFRD 117
Query: 136 LFS 138
L S
Sbjct: 118 LLS 120
>gnl|CDD|239455 cd03339, TCP1_epsilon, TCP-1 (CTT or eukaryotic type II) chaperonin
family, epsilon subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 526
Score = 28.8 bits (65), Expect = 1.0
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 13/84 (15%)
Query: 4 NSGYHPPPLYTADLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKI 63
NSG +P + + VK R K + +D++E V +T +SK
Sbjct: 456 NSGLNP-------IETLSEVKARQVKEKNPHLGIDCLGRGTNDMKEQ--KV-FETLISKK 505
Query: 64 KTLRLATSYISYLMKILETDDIIS 87
+ + LAT + ++KI DD+I
Sbjct: 506 QQILLATQVVKMILKI---DDVIV 526
>gnl|CDD|153090 cd08025, RNR_PFL_like_DUF711, Uncharacterized proteins with
similarity to Ribonucleotide reductase and Pyruvate
formate lyase. This subfamily contains Streptococcus
pneumoniae Sp0239 and similar uncharacterized proteins.
Sp0239 is structurally similar to ribonucleotide
reductase (RNR) and pyruvate formate lyase (PFL), which
are believed to have diverged from a common ancestor.
RNR and PFL possess a ten-stranded alpha-beta barrel
domain that hosts the active site, and are radical
enzymes. RNRs are found in all organisms and provide
the only mechanism by which nucleotides are converted
to deoxynucleotides. PFL is an essential enzyme in
anaerobic bacteria that catalyzes the conversion of
pyruvate and CoA to acteylCoA and formate.
Length = 400
Score = 28.4 bits (64), Expect = 1.2
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 38 QSINNAFSDLRECIPNVPSDTKLS-KIKTLRLATSYISYLMKILETDDIISI 88
+ I +A L E + V S +L I R++ + I+ L L+ +D + I
Sbjct: 43 EKITSAAKRLVETVEEVSS--ELGVPIVNKRISVTPIAILAAGLDAEDYVEI 92
>gnl|CDD|114155 pfam05414, DUF1717, Viral domain of unknown function (DUF1717).
This domain is found in viral proteins of unknown
function.
Length = 103
Score = 27.0 bits (59), Expect = 1.8
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 46 DLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKADLSNHSSHRKNK 105
DL++CI + D +S + + + ++ Y + I + D II ++D + H + KN
Sbjct: 14 DLKDCIEELNLDHGISH-ELIEVCCKFLGYEVHITKGDSIIKLNDDIEMAAIHIGYGKNG 72
Query: 106 SQYDSPSEISSNQSSQYVMDPSCQ 129
+ E S + C+
Sbjct: 73 HLFCINQERSKIPKDSQIKGNECE 96
>gnl|CDD|200439 cd11283, ADF_GMF-beta_like, ADF-homology domain of glia
maturation factor beta and related proteins. Actin
depolymerization factor/cofilin-like domains (ADF
domains) are present in a family of essential
eukaryotic actin regulatory proteins. Most of these
proteins enhance the turnover rate of actin and
interact with actin monomers as well as actin
filaments. The glia maturation factor (GMF), however,
does not bind actin but interacts with the Arp2/3
complex (which contains actin-related proteins, amongst
others) and suppresses Arp2/3 activity, inducing the
dissociation of branched daughter filaments from their
mother filaments. This family includes both mammalian
GMF isoforms, GMF-beta and GMF-gamma. GMF-beta
regulates cellular growth, fission, differentiation and
apoptosis. GMF-gamma is important in myeloid cell
development and is an important regulator for cell
migration and polarity in neutrophils.
Length = 122
Score = 26.8 bits (60), Expect = 2.2
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 12/57 (21%)
Query: 54 VPSDTKLSKIKTLRLATSYI-----------SYLMKILETDDIISIDDFKADLSNHS 99
+ + K +K R S + + E + ISI++ +L HS
Sbjct: 2 ISDEVK-EALKKFRFRKSKANAALILKIDKEKQEIVVDEELEDISIEELAEELPEHS 57
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 27.1 bits (60), Expect = 3.6
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 56 SDTKLSKIKTLRLATSYISYLMKILETDDIISIDDFKAD 94
S+ KLS + RLA L+ +LE DI+ +D++ AD
Sbjct: 445 SNLKLSTGQKKRLA-----LLLALLEERDILVLDEWAAD 478
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 26.7 bits (59), Expect = 4.6
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 54 VPSDTKLSKIKTLRLATS 71
VP+D ++ +KTLR+ S
Sbjct: 105 VPADIRVLSLKTLRVDQS 122
>gnl|CDD|177555 PHA03193, PHA03193, tegument protein VP11/12; Provisional.
Length = 594
Score = 26.6 bits (58), Expect = 4.7
Identities = 15/68 (22%), Positives = 27/68 (39%)
Query: 12 LYTADLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPSDTKLSKIKTLRLATS 71
LY + ++ ++ R NK R +N F L E + ++PSD
Sbjct: 236 LYMWAMWLMDLLDLRACPNKFGPRAPIDFDNIFLALAEAMGSLPSDKWADTALLCHFIEH 295
Query: 72 YISYLMKI 79
++ L+ I
Sbjct: 296 LLAPLIHI 303
>gnl|CDD|227551 COG5226, CEG1, mRNA capping enzyme, guanylyltransferase (alpha)
subunit [RNA processing and modification].
Length = 404
Score = 26.4 bits (58), Expect = 6.3
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 46 DLRECIPNVPSDTKLSKIKTLRLATSYISYLMKILET-DDIISIDD---FKADLSNHSSH 101
+ EC+ KL + + + ++IS + +LE+ D +SI+D F + + +S
Sbjct: 312 RIVECVLKKEGAWKLLRFRDDKDTPNHISVVCNVLESIRDNVSIEDLSTFYSVIRENSKR 371
Query: 102 RKNKSQYDSPSEISSN 117
R+ + P SN
Sbjct: 372 REKAMRRGRPLPSQSN 387
>gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 281
Score = 26.1 bits (58), Expect = 6.6
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 45 SDLRECIPNVPSDTK--LSKIKTLRLATSYISY 75
DL E I VP + K L K+K L I Y
Sbjct: 193 EDLDEVIELVPDEIKEELEKLKEL---AESIKY 222
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 26.0 bits (58), Expect = 8.9
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 7/62 (11%)
Query: 2 SYNSGY-----HPPPLYTADLPIIRVVKRRNTANKKERRRTQSINNAFSDLRECIPNVPS 56
SY G+ PP + A L IR +K N ++ + R + A IP +P+
Sbjct: 269 SYAPGFIFTTSLPPAIAAAALASIRHLKESNEERERHQERAAKLKAALDAAG--IPVMPN 326
Query: 57 DT 58
++
Sbjct: 327 ES 328
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
0.313 0.127 0.355
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: 6,675,400
Number of extensions: 547402
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 381
Number of HSP's successfully gapped: 29
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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: 54 (24.5 bits)