RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15513
(77 letters)
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain.
Length = 125
Score = 144 bits (366), Expect = 7e-47
Identities = 60/76 (78%), Positives = 69/76 (90%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
+A +GVRPC ISRQLRVSHGCVSKIL RYQETGSIRPGVIGGSKP+VATP+V ++I EYK
Sbjct: 29 LAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSIRPGVIGGSKPKVATPEVVKKIAEYK 88
Query: 61 GENPAMFSWEIRDRLV 76
ENP +F+WEIRDRL+
Sbjct: 89 RENPGIFAWEIRDRLL 104
>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
Length = 128
Score = 141 bits (358), Expect = 1e-45
Identities = 60/76 (78%), Positives = 68/76 (89%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
+A +G+RPC ISRQLRVSHGCVSKILNRY ETGSIRPG IGGSKPRVATP+V ++IE YK
Sbjct: 29 LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYK 88
Query: 61 GENPAMFSWEIRDRLV 76
ENP MF+WEIRDRL+
Sbjct: 89 QENPGMFAWEIRDRLL 104
>gnl|CDD|128645 smart00351, PAX, Paired Box domain.
Length = 125
Score = 137 bits (346), Expect = 8e-44
Identities = 56/76 (73%), Positives = 64/76 (84%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
+A GVRPC ISRQL VSHGCVSKIL RY ETGSIRPG IGGSKP+VATP V ++I +YK
Sbjct: 29 LAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88
Query: 61 GENPAMFSWEIRDRLV 76
ENP +F+WEIRDRL+
Sbjct: 89 QENPGIFAWEIRDRLL 104
>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain.
Length = 50
Score = 28.8 bits (65), Expect = 0.055
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 33
+ A G+ I+ L VS V + L RY+E G
Sbjct: 13 LLAEGLSVKEIAELLGVSRRTVYRWLKRYREGG 45
>gnl|CDD|225949 COG3415, COG3415, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 138
Score = 30.0 bits (68), Expect = 0.062
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 11 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEE 58
+++ VS V + + RY+ETG P +PR + + + E
Sbjct: 27 AAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLE 74
>gnl|CDD|222216 pfam13551, HTH_29, Winged helix-turn helix. This
helix-turn-helix domain is often found in transferases
and is likely to be DNA-binding.
Length = 109
Score = 29.2 bits (66), Expect = 0.095
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRVATPDVERRIEE 58
+ A GV I+R L +S V + L R+ E G +++ G +P+ E +
Sbjct: 7 LLAEGVSVAQIARLLGLSRRTVYRWLKRFNEGGLAALKDRPRSGRPRNRLSPEQEAALVA 66
Query: 59 YKGENPAM 66
E P
Sbjct: 67 LAREKPPE 74
>gnl|CDD|222226 pfam13565, HTH_32, Homeodomain-like domain.
Length = 74
Score = 27.3 bits (61), Expect = 0.31
Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 2/56 (3%)
Query: 22 VSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMF--SWEIRDRL 75
V + L RY+E G+ G P+ R I P ++L
Sbjct: 2 VYRWLKRYREEGAAGLVHRPGRPSNHRYPEELRAIVLTLIREPYADFGPTLAAEKL 57
>gnl|CDD|221778 pfam12802, MarR_2, MarR family. The Mar proteins are involved in
the multiple antibiotic resistance, a non-specific
resistance system. The expression of the mar operon is
controlled by a repressor, MarR. A large number of
compounds induce transcription of the mar operon. This
is thought to be due to the compound binding to MarR,
and the resulting complex stops MarR binding to the
DNA. With the MarR repression lost, transcription of
the operon proceeds. The structure of MarR is known and
shows MarR as a dimer with each subunit containing a
winged-helix DNA binding motif.
Length = 60
Score = 25.6 bits (57), Expect = 1.0
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 11 ISRQLRVSHGCVSKILNRYQETGSIR 36
++R+L +S VS+++ R +E G +
Sbjct: 25 LARRLGLSKQTVSRLVKRLEEKGLVE 50
>gnl|CDD|184154 PRK13573, PRK13573, anthranilate synthase component I; Provisional.
Length = 503
Score = 26.7 bits (59), Expect = 1.2
Identities = 12/24 (50%), Positives = 18/24 (75%), Gaps = 2/24 (8%)
Query: 34 SIRPGVIGGSKPRVATPDVERRIE 57
+IRP I G++PR ATP+ +R +E
Sbjct: 309 TIRP--IAGTRPRGATPEEDRALE 330
>gnl|CDD|172498 PRK13997, PRK13997, potassium-transporting ATPase subunit C;
Provisional.
Length = 193
Score = 25.3 bits (55), Expect = 2.9
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 16 RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75
R HG VS I + + +GS S P + VE+ IEE+K +NP++ E+ L
Sbjct: 68 RYFHGRVSSIEYKAEASGS---NNYAPSNPDLEK-RVEKSIEEWKKQNPSVPVTEVPIDL 123
Query: 76 V 76
V
Sbjct: 124 V 124
>gnl|CDD|235651 PRK05940, PRK05940, anthranilate synthase component I-like protein;
Validated.
Length = 463
Score = 25.1 bits (55), Expect = 4.0
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 34 SIRPGVIGGSKPRVATPDVERRIEE 58
RP I G++PR TP ++++ E
Sbjct: 268 QTRP--IAGTRPRGKTPAEDQQLAE 290
>gnl|CDD|184146 PRK13565, PRK13565, anthranilate synthase component I; Provisional.
Length = 490
Score = 24.9 bits (55), Expect = 5.5
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 25 ILNRYQETG--SIRPGVIGGSKPRVATPDVERRIEE 58
IL R QE ++RP I G++PR ATP+ + +E
Sbjct: 287 ILVR-QEDRIVTVRP--IAGTRPRGATPEEDLALET 319
>gnl|CDD|143331 cd01392, HTH_LacI, Helix-turn-helix (HTH) DNA binding domain of
the LacI family of transcriptional regulators. HTH-DNA
binding domain of the LacI (lactose operon repressor)
family of bacterial transcriptional regulators and
their putative homologs found in plants. The LacI
family has more than 500 members distributed among
almost all bacterial species. The monomeric proteins of
the LacI family contain common structural features that
include a small DNA-binding domain with a
helix-turn-helix motif in the N-terminus, a regulatory
ligand-binding domain which exhibits the type I
periplasmic binding protein fold in the C-terminus for
oligomerization and for effector binding, and an
approximately 18-amino acid linker connecting these two
functional domains. In LacI-like transcriptional
regulators, the ligands are monosaccharides including
lactose, ribose, fructose, xylose, arabinose,
galactose/glucose, and other sugars, with a few
exceptions. When the C-terminal domain of the LacI
family repressor binds its ligand, it undergoes a
conformational change which affects the DNA-binding
affinity of the repressor. In Escherichia coli, LacI
represses transcription by binding with high affinity
to the lac operon at a specific operator DNA sequence
until it interacts with the physiological inducer
allolactose or a non-degradable analog IPTG
(isopropyl-beta-D-thiogalactopyranoside). Induction of
the repressor lowers its affinity for the operator
sequence, thereby allowing transcription of the lac
operon structural genes (lacZ, lacY, and LacA). The lac
repressor occurs as a tetramer made up of two
functional dimers. Thus, two DNA binding domains of a
dimer are required to bind the inverted repeat
sequences of the operator DNA binding sites.
Length = 52
Score = 23.5 bits (52), Expect = 6.2
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 11 ISRQLRVSHGCVSKILN 27
I+R VS VS++LN
Sbjct: 3 IARAAGVSVATVSRVLN 19
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 24.7 bits (54), Expect = 6.5
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 25 ILNRYQETGSIRPGVIGGSKPRVAT 49
+L+RY G IR GV ++PR+ T
Sbjct: 933 LLHRYSGQGDIRIGVPNANRPRLET 957
>gnl|CDD|222191 pfam13518, HTH_28, Helix-turn-helix domain. This
helix-turn-helix domain is often found in transposases
and is likely to be DNA-binding.
Length = 52
Score = 23.3 bits (51), Expect = 7.6
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 11 ISRQLRVSHGCVSKILNRYQETG 33
+R+L +S V + + RY+E G
Sbjct: 18 AARKLGISRRTVYRWIKRYEEGG 40
>gnl|CDD|235309 PRK04596, minC, septum formation inhibitor; Reviewed.
Length = 248
Score = 24.1 bits (52), Expect = 7.9
Identities = 9/30 (30%), Positives = 19/30 (63%)
Query: 29 YQETGSIRPGVIGGSKPRVATPDVERRIEE 58
+++ G ++ G +G + R+ T DV R ++E
Sbjct: 7 FEQAGELKIGQVGIANLRIRTLDVPRLVQE 36
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 23.9 bits (52), Expect = 9.7
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 3/48 (6%)
Query: 29 YQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76
Y TG +P K + + + +Y GE+ + R +
Sbjct: 238 YLTTGKYKPPPTFAEKLDAILRHL-QLLADYYGESKGLR--IARKHIA 282
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
0.321 0.137 0.415
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,108,751
Number of extensions: 325179
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 18
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)