RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8831
(88 letters)
>gnl|CDD|214648 smart00401, ZnF_GATA, zinc finger binding to DNA consensus
sequence [AT]GATA[AG].
Length = 52
Score = 49.3 bits (118), Expect = 8e-10
Identities = 20/33 (60%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 15 RSGVSCANCSTTCTTLWRRNNNGE-PVCNACGL 46
SG SC+NC TT T LWRR +G +CNACGL
Sbjct: 1 GSGRSCSNCGTTETPLWRRGPSGNKTLCNACGL 33
>gnl|CDD|109380 pfam00320, GATA, GATA zinc finger. This domain uses four
cysteine residues to coordinate a zinc ion. This domain
binds to DNA. Two GATA zinc fingers are found in the
GATA transcription factors. However there are several
proteins which only contains a single copy of the
domain.
Length = 36
Score = 46.5 bits (111), Expect = 6e-09
Identities = 17/28 (60%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 20 CANCSTTCTTLWRRNNNGEP-VCNACGL 46
C+NC TT T LWRR +G +CNACGL
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGL 28
>gnl|CDD|238123 cd00202, ZnF_GATA, Zinc finger DNA binding domain; binds
specifically to DNA consensus sequence [AT]GATA[AG]
promoter elements; a subset of family members may also
bind protein; zinc-finger consensus topology is
C-X(2)-C-X(17)-C-X(2)-C.
Length = 54
Score = 46.2 bits (110), Expect = 1e-08
Identities = 17/29 (58%), Positives = 21/29 (72%), Gaps = 1/29 (3%)
Query: 19 SCANCSTTCTTLWRRN-NNGEPVCNACGL 46
+C+NC TT T LWRR + G +CNACGL
Sbjct: 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGL 29
>gnl|CDD|227928 COG5641, GAT1, GATA Zn-finger-containing transcription factor
[Transcription].
Length = 498
Score = 32.5 bits (74), Expect = 0.015
Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 19 SCANCSTTCTTLWRR-----NNNGEPVCNACGL 46
C+NC TT T LWRR + G +CNACGL
Sbjct: 160 VCSNCKTTSTPLWRRASSESSLPGNNLCNACGL 192
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 28.8 bits (65), Expect = 0.23
Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 19 SCANCSTTCTTLWRRNNNGEPVCNACGLI 47
SC C T + GE VC CGL+
Sbjct: 3 SCPECG--STNIITDYERGEIVCADCGLV 29
>gnl|CDD|107269 cd06274, PBP1_FruR, Ligand binding domain of DNA transcription
repressor specific for fructose (FruR) and its close
homologs. Ligand binding domain of DNA transcription
repressor specific for fructose (FruR) and its close
homologs, all of which are a member of the LacI-GalR
family of bacterial transcription regulators. The
LacI-GalR family repressors are composed of two
functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal
ligand-binding domain, which is homologous to members
of the type I periplasmic binding protein superfamily.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcription
repressor undergoes a conformational change upon ligand
binding which in turn changes the DNA binding affinity
of the repressor.
Length = 264
Score = 27.9 bits (63), Expect = 0.56
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 56 PEKIMPPIESMISRNGDALSVITSTPN 82
PE +E++I+R DAL V S P
Sbjct: 41 PETERETVETLIARQVDALIVAGSLPP 67
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription
factor TFIIB contains a zinc-binding motif near the
N-terminus. This domain is involved in the interaction
with RNA pol II and TFIIF and plays a crucial role in
selecting the transcription initiation site. The domain
adopts a zinc ribbon like structure.
Length = 40
Score = 26.1 bits (58), Expect = 0.74
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI 53
C NC +T GE VC CGL++ I
Sbjct: 3 CPNCGSTEIV--FDYERGEYVCTECGLVLEDNII 34
>gnl|CDD|240262 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 27.5 bits (61), Expect = 0.84
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 37 GEPVCNACGLIMNTVDINAPEKIMPPI 63
G +CN C N I + MPPI
Sbjct: 129 GRRICNTCNRNFNIAHIRSDPYDMPPI 155
>gnl|CDD|179503 PRK02929, PRK02929, L-arabinose isomerase; Provisional.
Length = 499
Score = 26.3 bits (59), Expect = 1.8
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 46 LIMNTVDINAPEKIMP 61
LI+N VD P +P
Sbjct: 404 LIVNEVDAVEPPHPLP 419
>gnl|CDD|217690 pfam03718, Glyco_hydro_49, Glycosyl hydrolase family 49. Family of
dextranase (EC 3.2.1.11) and isopullulanase (EC
3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic
bonds in dextran polymers.
Length = 566
Score = 26.4 bits (58), Expect = 2.1
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 10/59 (16%)
Query: 21 ANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDINAPEKIMPPIESMISRNGDALSVITS 79
NC +TC +W N+ G T+D+ PP SM G++ +I+
Sbjct: 294 VNCHSTCLRMWWFNSLGG---------GQTLDLVGVTISAPPFNSMDF-YGNSGDLISM 342
>gnl|CDD|222929 PHA02779, PHA02779, E6 protein; Provisional.
Length = 150
Score = 26.0 bits (57), Expect = 2.3
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 21 ANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDIN 54
AN STT T+ + +C C L M+T+ IN
Sbjct: 4 ANASTTARTIDQ-------LCKQCNLTMHTLQIN 30
>gnl|CDD|152198 pfam11762, Arabinose_Iso_C, L-arabinose isomerase C-terminal
domain. This is a family of L-arabinose isomerases,
AraA, EC:5.3.1.4. These enzymes catalyze the reaction:
L-arabinose <=> L-ribulose. This reaction is the first
step in the pathway of L-arabinose utilisation as a
carbon source after entering the cell L-arabinose is
converted into L-ribulose by the L-arabinose isomerases
enzyme. This is a C-terminal non catalytic domain.
Length = 115
Score = 25.6 bits (57), Expect = 2.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 46 LIMNTVDINAPEKIMP 61
LI+N VD PE +P
Sbjct: 44 LIVNEVDAVKPEADLP 59
>gnl|CDD|188237 TIGR02634, xylF, D-xylose ABC transporter, substrate-binding
protein. Members of this family are periplasmic (when
in Gram-negative bacteria) binding proteins for
D-xylose import by a high-affinity ATP-binding cassette
(ABC) transporter [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 302
Score = 25.2 bits (55), Expect = 4.5
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 57 EKIMPPIESMISRNGDALSVI 77
K + IE++I+R D L +I
Sbjct: 41 AKQISQIENLINRGVDVLVII 61
>gnl|CDD|190568 pfam03214, RGP, Reversibly glycosylated polypeptide.
Length = 348
Score = 25.2 bits (55), Expect = 5.8
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 37 GEPVCNACGLIMNTVDINAPEKIMPPIESMISRNGDALSVITSTP 81
G +CGL +N D +AP + + P + RN + + + P
Sbjct: 156 GVTCALSCGLWLNLADYDAPTQAVKPKQ----RNTRYVDAVMTVP 196
>gnl|CDD|179734 PRK04059, rpl34e, 50S ribosomal protein L34e; Validated.
Length = 88
Score = 24.2 bits (53), Expect = 6.3
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 31 WRRNNNGEPVCNACGLIMNTVDINAPEKI 59
+ R + C CG +N V P +I
Sbjct: 27 YERKKPSKAKCAICGKPLNGVPRGRPVEI 55
>gnl|CDD|171592 PRK12575, PRK12575, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 235
Score = 24.9 bits (54), Expect = 6.4
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 8 REQTGNKRSGVSCANCSTTCTTLW 31
REQ + CA CST C + W
Sbjct: 137 REQLDGLYECILCACCSTACPSYW 160
>gnl|CDD|211677 TIGR01660, narH, nitrate reductase, beta subunit. The Nitrate
reductase enzyme complex allows bacteria to use nitrate
as an electron acceptor during anaerobic growth. The
enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone
pool and transfers them to the beta subunit. This model
is specific for the beta subunit for nitrate reductase
I (narH) and nitrate reductase II (narY) for gram
positive and gram negative bacteria.A few thermophiles
and archaea also match the model.The seed members used
in this model are all experimentally characterized and
include the following:SP:P11349, and SP:P19318, both
E.Coli (NarH and NarY respectively), SP:P42176 from B.
Subtilis, GP:11344602 from Psuedomonas
fluorescens,GP:541762 from Paracoccus denitrificans,
and GP:18413622 from Halomonas halodenitrificans. This
model also matches PFAM pfam00037 for 4Fe-4S binding
domain [Energy metabolism, Anaerobic].
Length = 492
Score = 24.8 bits (54), Expect = 6.5
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 7 IREQTG---NKRSGVSCANCSTTCTTLW 31
IR Q G N + C CS TC +W
Sbjct: 3 IRSQIGMVLNLDKCIGCHTCSVTCKNVW 30
>gnl|CDD|226314 COG3791, COG3791, Uncharacterized conserved protein [Function
unknown].
Length = 133
Score = 24.3 bits (53), Expect = 7.7
Identities = 12/69 (17%), Positives = 20/69 (28%), Gaps = 8/69 (11%)
Query: 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDINAPEKIMPPIESMISRNGDALSVITS 79
C C WR + V G+ +D PE + P ++ + L +
Sbjct: 72 CPTCG--SPLFWRGPDEDPFV----GVNAGALD--DPEFLPPQVQIFVGSKLPWLDIADD 123
Query: 80 TPNIHHSDD 88
P
Sbjct: 124 LPRFEGDPY 132
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 0.131 0.407
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,175,459
Number of extensions: 303679
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 306
Number of HSP's successfully gapped: 27
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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: 53 (24.3 bits)