RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3614
(209 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 = 63.0 bits (154), Expect = 9e-14
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 31 YRKVMKPMLERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRR 90
R+ + ER+RR RIN DEL+ L+ T KL KA+IL V +++ ++
Sbjct: 3 SRREAHNLRERRRRERINDAFDELRSLLPTL-----PPSKKLSKAEILRKAVDYIKSLQE 57
Query: 91 QQR 93
+
Sbjct: 58 LLQ 60
>gnl|CDD|128787 smart00511, ORANGE, Orange domain. This domain confers specificity
among members of the Hairy/E(SPL) family.
Length = 45
Score = 60.6 bits (148), Expect = 6e-13
Identities = 19/41 (46%), Positives = 28/41 (68%)
Query: 105 FRAGFTTCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEM 145
FR+G+ CANEVS+ L+ PG D + +L+SHL LN++
Sbjct: 3 FRSGYRECANEVSRFLSQLPGTDPDVRARLLSHLQTHLNQL 43
>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 = 59.9 bits (146), Expect = 8e-13
Identities = 19/42 (45%), Positives = 29/42 (69%)
Query: 104 RFRAGFTTCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEM 145
+FRAGF C NEV++ L+S G+D + +L+SHL LN++
Sbjct: 1 KFRAGFRECLNEVARFLSSVEGVDPDVRARLLSHLASCLNQL 42
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 60.2 bits (147), Expect = 8e-13
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 32 RKVMKPMLERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMR 89
R+ ER+RR RIN +EL++L+ T KL KA+IL L +++++ ++
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTP------PNKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 57.6 bits (140), Expect = 8e-12
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 37 PMLERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQR 93
ER+RR +IN DEL+ L+ T KL KA+IL L +++++ ++ + +
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLP-----KNKKLSKAEILRLAIEYIKSLQEELQ 52
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 30.4 bits (69), Expect = 0.76
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 123 TPGIDLRLGTKLMSHLGQRLNEMDKISPLSVRVMDVCTP 161
T GI RLGT ++ LG +EMD+++ L V+V+ TP
Sbjct: 412 TSGI--RLGTPALTTLGMGSDEMDEVAELIVKVLSNTTP 448
>gnl|CDD|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA
binding. This is the middle region of a family of TATA
element modulatory factor 1 proteins conserved in
eukaryotes that contains at its N-terminal section a
number of leucine zippers that could potentially form
coiled coil structures. The whole proteins bind to the
TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding
of TATA binding protein. TMFs are evolutionarily
conserved golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells.
Length = 74
Score = 27.7 bits (62), Expect = 1.1
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 55 KDLMVTALQAEGENVSKLEKA 75
KD + L EGE +SK E
Sbjct: 10 KDEQIAQLMEEGEKLSKKELK 30
>gnl|CDD|183573 PRK12524, PRK12524, RNA polymerase sigma factor; Provisional.
Length = 196
Score = 29.1 bits (65), Expect = 1.4
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 28 TYQYRKVMKPMLERKRRARINRC-LDELKDLMVTALQAEGENVSKLEKADILELTVQHLQ 86
T+ YR V +R RR R LD+ + A AE E + + ++ L+ + L
Sbjct: 80 TWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAE-EALIEGDRMRALDAALAALP 138
Query: 87 KMRRQ 91
+ +RQ
Sbjct: 139 ERQRQ 143
>gnl|CDD|227016 COG4670, COG4670, Acyl CoA:acetate/3-ketoacid CoA transferase
[Lipid metabolism].
Length = 527
Score = 29.2 bits (66), Expect = 1.5
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 140 QRLNEMDKISPLSVRV----MD--VCTPPPSPHSDTYSMPLTPASSGSSQVDT 186
+R+ + + P VRV +D + P H T S P PA SG +
Sbjct: 216 KRVVKKGTLKPKDVRVPGILVDYVIVVEDPEDHWQTGSTPYNPAISGEIFIPL 268
>gnl|CDD|223399 COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA
replication, recombination, and repair].
Length = 581
Score = 28.4 bits (64), Expect = 3.3
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 46 RINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRLASNPVTDADRF 105
+ + L EL++ M A + E+A L ++ L+K++ +Q ++ + D D
Sbjct: 199 KDDAVLQELEEKMEEASENL-----DFERAARLRDQIKALEKLQEKQAVSLFKLQDLDVI 253
>gnl|CDD|217697 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA
binding domain. This family contains the RNA binding
domain of Polyribonucleotide nucleotidyltransferase
(PNPase) PNPase is involved in mRNA degradation in a
3'-5' direction.
Length = 80
Score = 26.5 bits (59), Expect = 3.7
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 45 ARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQK--MRRQ 91
R LDE+K +V A AE + + + E I + L+K +R +
Sbjct: 25 ERYAA-LDEIKADVVAAFAAEDDELDEKEIKAIF----KALEKKVVRSR 68
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial
pseudouridine synthases similar to E. coli TruA. This
group consists of eukaryotic and bacterial pseudouridine
synthases similar to E. coli TruA, Pseudomonas
aeruginosa truA and human pseudouridine synthase-like 1
(PUSL1). Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruA makes psi38/39 and/or 40 in tRNA.
psi38 and psi39 in tRNAs are highly phylogenetically
conserved. P. aeruginosa truA is required for induction
of type III secretory genes and may act through
modifying tRNAs critical for the expression of type III
genes or their regulators.
Length = 239
Score = 27.4 bits (62), Expect = 4.2
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 25 ISRTYQYR---KVMKPMLERKRRARINRCLDELKDLMVTALQ 63
SRTY+YR + + R+ + R LD + M A +
Sbjct: 101 KSRTYRYRILNRPVPSPFLRRYVWHVPRPLDI--EAMQEAAK 140
>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA
binding. This is the C-terminal conserved coiled coil
region of a family of TATA element modulatory factor 1
proteins conserved in eukaryotes. The proteins bind to
the TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding of
TATA binding protein. TMF1_TATA_bd is the most conserved
part of the TMFs. TMFs are evolutionarily conserved
golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells. The Rab6-binding
domain appears to be the same region as this C-terminal
family.
Length = 121
Score = 26.8 bits (60), Expect = 4.3
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 42 KRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQ 92
K + + L++L+ T L+ GE K E+ + L V L++M R+Q
Sbjct: 69 KEIEELEKELEDLEQRYETTLELLGE---KSERVEELRADVVDLKEMYREQ 116
>gnl|CDD|237523 PRK13825, PRK13825, conjugal transfer protein TraB; Provisional.
Length = 388
Score = 27.7 bits (62), Expect = 4.4
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 10/40 (25%)
Query: 180 GSSQVDTCDYTS----------QYKMYESMPSPKSVWRPW 209
G++ VD Y + + E MP P S+W+PW
Sbjct: 258 GAAVVDPGGYDNVLVAISAGGGRILYRERMPVPVSMWQPW 297
>gnl|CDD|131524 TIGR02471, sucr_syn_bact_C, sucrose phosphate synthase, sucrose
phosphatase-like domain, bacterial. Sucrose phosphate
synthase (SPS) and sucrose phosphate phosphatase (SPP)
are the last two enzymes of sucrose biosynthesis. In
cyanobacteria and plants, the C-terminal region of most
or all versions of SPS has a domain homologous to the
known SPP. This domain may serve a binding or regulatory
rather than catalytic function. Sequences in this family
are bacterial C-terminal regions found in all but two of
the putative bacterial sucrose phosphate synthases
described by TIGR02472.
Length = 236
Score = 27.4 bits (61), Expect = 5.1
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 43 RRARINRCLDELKDLMVTALQAEGEN----VSKLEKADILELTVQHLQKMRRQQRLASNP 98
RR + L ++ L LQ + E +S L + E + +++ RQQ A+
Sbjct: 88 RRQAVVEALADIPGL---TLQDDQEQGPFKISYLLDPEG-EPILPQIRQRLRQQSQAAKV 143
Query: 99 V 99
+
Sbjct: 144 I 144
>gnl|CDD|99733 cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). SHMT
carries out interconversion of serine and glycine; it
catalyzes the transfer of hydroxymethyl group of N5,
N10-methylene tetrahydrofolate to glycine resulting in
the formation of serine and tetrahydrofolate. Both
eukaryotic and prokaryotic SHMT enzymes form tight
obligate homodimers; the mammalian enzyme forms a
homotetramer comprising four pyridoxal phosphate-bound
active sites.
Length = 402
Score = 27.6 bits (62), Expect = 5.4
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 111 TCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEMDKISPLSVRV 155
T + S GI R+GT M+ G EM++I+ R
Sbjct: 341 TLPWDPSSPF-VPSGI--RIGTPAMTTRGMGEEEMEEIADFIARA 382
>gnl|CDD|162300 TIGR01317, GOGAT_sm_gam, glutamate synthases, NADH/NADPH, small
subunit. This model represents one of three built for
the NADPH-dependent or NADH-dependent glutamate
synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small
subunit or homologous region. TIGR01316 describes a
family in several archaeal and deeply branched
bacterial lineages of a homotetrameric form for which
there is no large subunit. Another model describes
glutamate synthase small subunit from gamma and some
alpha subdivision Proteobacteria plus paralogs of
unknown function. This model describes the small
subunit, or homologous region of longer forms proteins,
of eukaryotes, Gram-positive bacteria, cyanobacteria,
and some other lineages. All members with known
function participate in NADH or NADPH-dependent
reactions to interconvert between glutamine plus
2-oxoglutarate and two molecules of glutamate.
Length = 485
Score = 27.5 bits (61), Expect = 5.7
Identities = 6/33 (18%), Positives = 15/33 (45%)
Query: 20 EQLQPISRTYQYRKVMKPMLERKRRARINRCLD 52
+ P +R +++ P + + + RC+D
Sbjct: 14 TERDPRTRLKDWKEFTNPFDKESAKYQAARCMD 46
>gnl|CDD|240389 PTZ00374, PTZ00374, dihydroxyacetone phosphate acyltransferase;
Provisional.
Length = 1108
Score = 27.1 bits (60), Expect = 7.3
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 43 RRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRL 94
R ++ R + E++ L+AE + ++ DIL+ V+ L++M+R ++
Sbjct: 1060 RLQQLMRHVCEMRSSSPHLLRAEEQKKAR---EDILKEYVKVLRRMKRPSKM 1108
>gnl|CDD|214333 CHL00013, rpoA, RNA polymerase alpha subunit.
Length = 327
Score = 26.8 bits (60), Expect = 7.7
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 14/56 (25%)
Query: 7 ENQINMINNTVDIEQLQPISRTYQYRKVMKPMLERKRRARINRCLDELK----DLM 58
+N+ + + IEQL+ R Y K RA I+ LD L DL+
Sbjct: 253 KNKKEIALKQIFIEQLELSVRAYNCLK----------RANIHTLLDLLNYSQEDLL 298
>gnl|CDD|139237 PRK12802, PRK12802, flagellin; Provisional.
Length = 282
Score = 26.8 bits (59), Expect = 7.7
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 78 LELTVQHLQKMRR---QQRLASNPVTDADRFRAGFTTCANEVSKCLAST 123
L+ + LQ+MR Q R SN TD FTT +E+++ ST
Sbjct: 82 LQESTNILQRMRELAVQSRNDSNDSTDRAALNKEFTTMLDEITRIATST 130
>gnl|CDD|193414 pfam12941, HCV_NS5a_C, HCV NS5a protein C-terminal region. This is
a family of proteins found in the hepatitis C virus.
This family contains the C-terminal region of the NS5A
protein. CC The molecular function of the non-structural
5a protein is uncertain. The NS5a protein is
phosphorylated when expressed in mammalian cells. It is
thought to interact with the ds RNA dependent
(interferon inducible) kinase PKR.
Length = 244
Score = 26.6 bits (59), Expect = 10.0
Identities = 17/41 (41%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 161 PPPSPHSDTYSMPLTPASSGSSQVDT-CDYTSQYKMYESMP 200
P PSP SD L+ SS SS+ D S Y SMP
Sbjct: 176 PQPSPSSDESDSGLSTPSSTSSEPPGEDDDASDAGSYSSMP 216
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
0.317 0.129 0.377
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,333,733
Number of extensions: 924113
Number of successful extensions: 1055
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1051
Number of HSP's successfully gapped: 33
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.6 bits)