RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1904
(163 letters)
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain.
Length = 125
Score = 150 bits (380), Expect = 1e-47
Identities = 61/92 (66%), Positives = 73/92 (79%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A +GVRPC ISRQLRVSHGCVSKIL RYQETGSIRPGVIGGSKP+VATP+V K+I EYK
Sbjct: 29 LAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSIRPGVIGGSKPKVATPEVVKKIAEYK 88
Query: 61 KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
+ NP I +WE+RD+L+ D+ + S I
Sbjct: 89 RENPGIFAWEIRDRLLAEGVCDNDNVPSVSSI 120
>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
Length = 128
Score = 144 bits (366), Expect = 2e-45
Identities = 60/92 (65%), Positives = 73/92 (79%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A +G+RPC ISRQLRVSHGCVSKILNRY ETGSIRPG IGGSKPRVATP+V K+IE YK
Sbjct: 29 LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYK 88
Query: 61 KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
+ NP + +WE+RD+L++ D S+ S I
Sbjct: 89 QENPGMFAWEIRDRLLQEGVCDKSNVPSVSSI 120
>gnl|CDD|128645 smart00351, PAX, Paired Box domain.
Length = 125
Score = 137 bits (348), Expect = 1e-42
Identities = 54/77 (70%), Positives = 63/77 (81%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A GVRPC ISRQL VSHGCVSKIL RY ETGSIRPG IGGSKP+VATP V K+I +YK
Sbjct: 29 LAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88
Query: 61 KTNPNITSWEVRDKLIK 77
+ NP I +WE+RD+L+
Sbjct: 89 QENPGIFAWEIRDRLLS 105
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 67.9 bits (167), Expect = 3e-16
Identities = 26/45 (57%), Positives = 32/45 (71%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RTTFT QLEELEK F+++ YP RE LA K G+TE +V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 62.3 bits (152), Expect = 7e-14
Identities = 25/46 (54%), Positives = 33/46 (71%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
+RR RT+FT QLEELEK FQ++ YP RE LA K G++E +V+
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 61.9 bits (151), Expect = 1e-13
Identities = 24/45 (53%), Positives = 31/45 (68%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RT FT QLEELEK F+++ YP RE LA + G+TE +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 42.0 bits (99), Expect = 2e-05
Identities = 19/72 (26%), Positives = 27/72 (37%)
Query: 72 RDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREAL 131
K + DS+ + E + R T QL LE+ F+ + YP TR L
Sbjct: 25 TTKNKREVEAADSEMKLERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKL 84
Query: 132 ANKFGMTETRVQ 143
+ M VQ
Sbjct: 85 SLLLNMPPKSVQ 96
>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain.
Length = 50
Score = 30.0 bits (68), Expect = 0.085
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 = 31.2 bits (71), Expect = 0.11
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 11 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 58
+++ VS V + + RY+ETG P +PR + + + + E
Sbjct: 27 AAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLE 74
>gnl|CDD|222226 pfam13565, HTH_32, Homeodomain-like domain.
Length = 74
Score = 29.6 bits (67), Expect = 0.17
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 2/58 (3%)
Query: 22 VSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNP--NITSWEVRDKLIK 77
V + L RY+E G+ G P+ + I P + +KL +
Sbjct: 2 VYRWLKRYREEGAAGLVHRPGRPSNHRYPEELRAIVLTLIREPYADFGPTLAAEKLAE 59
>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 = 28.4 bits (64), Expect = 0.74
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRVATPDVEKRIEE 58
+ A GV I+R L +S V + L R+ E G +++ G +P+ E +
Sbjct: 7 LLAEGVSVAQIARLLGLSRRTVYRWLKRFNEGGLAALKDRPRSGRPRNRLSPEQEAALVA 66
Query: 59 YKKTNP 64
+ P
Sbjct: 67 LAREKP 72
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 28.9 bits (65), Expect = 1.1
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQ 144
R +T A +E+LE+ + R+ T + +A + GMTE V+
Sbjct: 105 REKTKKVEAAIEKLEQRYMRN-----VTPKEVAAELGMTEEEVEA 144
>gnl|CDD|172498 PRK13997, PRK13997, potassium-transporting ATPase subunit C;
Provisional.
Length = 193
Score = 28.4 bits (63), Expect = 1.5
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 16 RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKL 75
R HG VS I + + +GS S P + VEK IEE+KK NP++ EV L
Sbjct: 68 RYFHGRVSSIEYKAEASGS---NNYAPSNPDLEK-RVEKSIEEWKKQNPSVPVTEVPIDL 123
Query: 76 IKVS 79
+ S
Sbjct: 124 VTNS 127
>gnl|CDD|179711 PRK04017, PRK04017, hypothetical protein; Provisional.
Length = 132
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 51 DVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRK 97
++ K++ EY + E+R +L + + D D ES V K +
Sbjct: 80 ELAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLR 126
>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 = 3.5
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|219851 pfam08456, Vmethyltransf_C, Viral methyltransferase C-terminal.
This domain is found to the C-terminus of the viral
methyltransferase domain (pfam01660) in
single-stranded-RNA positive-strand viruses with no DNA
stage in the Virgaviridae family.
Length = 208
Score = 27.1 bits (60), Expect = 4.5
Identities = 13/56 (23%), Positives = 24/56 (42%)
Query: 54 KRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQ 109
+ EEY++ I+ V DKL S++ S+ + K ++R S +
Sbjct: 93 RLYEEYERERKRISRKIVSDKLEVSEDGSASESSSDLKELRKFRRRASFEDLKEGE 148
>gnl|CDD|184154 PRK13573, PRK13573, anthranilate synthase component I; Provisional.
Length = 503
Score = 27.4 bits (61), Expect = 4.5
Identities = 11/24 (45%), Positives = 18/24 (75%), Gaps = 2/24 (8%)
Query: 34 SIRPGVIGGSKPRVATPDVEKRIE 57
+IRP I G++PR ATP+ ++ +E
Sbjct: 309 TIRP--IAGTRPRGATPEEDRALE 330
>gnl|CDD|217481 pfam03303, WTF, WTF protein. This is a family of hypothetical
Schizosaccharomyces pombe proteins. Their function is
unknown.
Length = 240
Score = 26.8 bits (59), Expect = 5.6
Identities = 5/30 (16%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 43 SKPRVATPDVEKRIEEYKKTNPNITSWEVR 72
A P+ + E+ + N + W ++
Sbjct: 55 GPTETANPNTHRE-NEFSDSADNSSPWLLK 83
>gnl|CDD|221901 pfam13027, DUF3888, Protein of unknown function (DUF3888). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 111 and 149 amino
acids in length.
Length = 88
Score = 25.7 bits (57), Expect = 6.2
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 49 TPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDT 86
P + K IE+Y +P+ + V K+++V R+ T
Sbjct: 10 APYISKAIEKYYGKDPSYSPTCV--KILEVKRIYGKGT 45
>gnl|CDD|212000 TIGR04277, squa_tetra_cyc, squalene--tetrahymanol cyclase. This
enzyme, also called squalene--tetrahymanol cyclase,
occurs a small number of eukaryotes, some of them
anaerobic. The pathway can occur under anaerobic
conditions, and the product is thought to replace
sterols, letting organisms with this compound build
membrane suitable for performing phagocytosis.
Length = 624
Score = 26.9 bits (59), Expect = 6.3
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 32 TGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVR 72
T I G +G + ++K I+ + T SWE R
Sbjct: 440 TAHILEG-LGEFGDQANHDQIQKMIKYFMDTQEKFGSWEAR 479
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is
a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner mitochondrial
membrane. The main function of the complex is to
transport electrons from NADH to ubiquinone, which is
accompanied by the translocation of protons from the
mitochondrial matrix to the inter membrane space.
Length = 219
Score = 26.5 bits (59), Expect = 6.9
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 93 VLKRKQRRSRT---TFTSAQLEELEKSFQRSHYPDI 125
V KR ++R TSA L+++E +++++ P+I
Sbjct: 156 VQKRIKKRGDPHEMKVTSAYLQDIENAYKKTFLPEI 191
>gnl|CDD|214699 smart00503, SynN, Syntaxin N-terminal domain. Three-helix domain
that (in Sso1p) slows the rate of its reaction with the
SNAP-25 homologue Sec9p.
Length = 117
Score = 25.8 bits (57), Expect = 8.1
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 14/80 (17%)
Query: 70 EVRDKLIKVSR-----LDDSDTESEPGIVLKRKQR--RSRTTFTSAQLEELEKSFQR--- 119
++ + ++ + L D + E L+R + A+L+ELEK
Sbjct: 19 KISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRA 78
Query: 120 SHYPDIYTR----EALANKF 135
S TR E L KF
Sbjct: 79 SGSASDRTRKAQTEKLRKKF 98
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 26.1 bits (58), Expect = 8.9
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 126 YTREALANKFGMTETRVQQFV 146
Y G+TE V+Q++
Sbjct: 265 YAEYLYPGILGLTEDLVKQYI 285
>gnl|CDD|115202 pfam06530, Phage_antitermQ, Phage antitermination protein Q. This
family consists of several phage antitermination protein
Q and related bacterial sequences. Antiterminator
proteins control gene expression by recognising control
signals near the promoter and preventing transcriptional
termination which would otherwise occur at sites that
may be a long way downstream.
Length = 126
Score = 25.5 bits (56), Expect = 9.2
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 120 SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157
S+Y ++ A+A ++G + TR+++ + GF+ CL
Sbjct: 73 SYYVHGSSKRAIARRYGCSVTRIRKRLCKAEGFIDGCL 110
>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 = 24.3 bits (54), Expect = 9.4
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 16/48 (33%)
Query: 11 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 58
I+R VS VS++LN KPRV+ + +R+
Sbjct: 3 IARAAGVSVATVSRVLNG---------------KPRVS-EETRERVLA 34
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 0.132 0.376
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,322,459
Number of extensions: 756359
Number of successful extensions: 828
Number of sequences better than 10.0: 1
Number of HSP's gapped: 827
Number of HSP's successfully gapped: 42
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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 (21.6 bits)
S2: 55 (25.0 bits)