RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10745
(197 letters)
>gnl|CDD|128645 smart00351, PAX, Paired Box domain.
Length = 125
Score = 120 bits (303), Expect = 2e-35
Identities = 50/56 (89%), Positives = 50/56 (89%)
Query: 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
HGGVNQLGGVFVNGRPLPD RQRIVELA NGVRPCDISRQL VSHGCVSKIL R
Sbjct: 1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGR 56
Score = 118 bits (297), Expect = 2e-34
Identities = 51/67 (76%), Positives = 57/67 (85%)
Query: 14 RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
RYYETGS + G IGGSKPKVAT VV IA YK+ENP +FAWEIRDRLL+EG+C +DNVP
Sbjct: 56 RYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVP 115
Query: 74 SVSSINR 80
SVSSINR
Sbjct: 116 SVSSINR 122
>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
Length = 128
Score = 118 bits (297), Expect = 2e-34
Identities = 48/55 (87%), Positives = 52/55 (94%)
Query: 119 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
GGVNQLGGVFVNGRPLPD +RQRIVELA +G+RPCDISRQLRVSHGCVSKIL+R
Sbjct: 2 QGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNR 56
Score = 112 bits (283), Expect = 2e-32
Identities = 49/69 (71%), Positives = 55/69 (79%)
Query: 14 RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
RYYETGS + G IGGSKP+VAT VV I YK+ENP MFAWEIRDRLL EG+C + NVP
Sbjct: 56 RYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVP 115
Query: 74 SVSSINRYI 82
SVSSINR +
Sbjct: 116 SVSSINRIL 124
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain.
Length = 125
Score = 114 bits (286), Expect = 8e-33
Identities = 47/56 (83%), Positives = 51/56 (91%)
Query: 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
G VNQLGGVFVNGRPLP+ +RQ+IVELAH+GVRPCDISRQLRVSHGCVSKIL R
Sbjct: 1 GQGRVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISRQLRVSHGCVSKILGR 56
Score = 111 bits (279), Expect = 7e-32
Identities = 52/69 (75%), Positives = 57/69 (82%)
Query: 14 RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
RY ETGS + GVIGGSKPKVAT VV IA YKRENP +FAWEIRDRLLAEG+C DNVP
Sbjct: 56 RYQETGSIRPGVIGGSKPKVATPEVVKKIAEYKRENPGIFAWEIRDRLLAEGVCDNDNVP 115
Query: 74 SVSSINRYI 82
SVSSI+R +
Sbjct: 116 SVSSISRIL 124
>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and
similar prokaryotic, metal regulated homodimeric
repressors. ARSR subfamily of helix-turn-helix bacterial
transcription regulatory proteins (winged helix
topology). Includes several proteins that appear to
dissociate from DNA in the presence of metal ions.
Length = 78
Score = 34.6 bits (80), Expect = 0.004
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 132 GRPLPDVVRQRIVE-LAHNGVRPCDISRQLRVSHGCVSKILS--RESNLHNYRLVREEGC 188
+ L D R RI+ L + +++ +L +S VS+ L E+ L R
Sbjct: 1 LKALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVY 60
Query: 189 FELSDLE 195
+ L+D E
Sbjct: 61 YSLTDAE 67
>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain.
Length = 50
Score = 31.9 bits (73), Expect = 0.024
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 140 RQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
R I+ L G+ +I+ L VS V + L R
Sbjct: 7 RAEILLLLAEGLSVKEIAELLGVSRRTVYRWLKR 40
>gnl|CDD|193235 pfam12759, HTH_Tnp_IS1, InsA C-terminal domain. This short domain
is found at the C-terminus of the InsA protein. This
domain contains a helix-turn-helix domain.
Length = 50
Score = 29.8 bits (67), Expect = 0.12
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 139 VRQRIVELAHNGVRPCDISRQLRVSHGCVSKIL 171
+++IV++A NG +R L++ V + L
Sbjct: 14 TKEQIVDMAMNGAGCRYTARTLKIGINTVIRTL 46
>gnl|CDD|182927 PRK11050, PRK11050, manganese transport regulator MntR;
Provisional.
Length = 152
Score = 29.6 bits (67), Expect = 0.64
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 146 LAHNG-VRPCDISRQLRVSHGCVSKILSR 173
+A G R DI+ +L VS V+K+L R
Sbjct: 46 IAEVGEARQVDIAARLGVSQPTVAKMLKR 74
>gnl|CDD|114760 pfam06056, Terminase_5, Putative ATPase subunit of terminase
(gpP-like). This family of proteins are annotated as
ATPase subunits of phage terminase after. Terminases are
viral proteins that are involved in packaging viral DNA
into the capsid.
Length = 58
Score = 27.7 bits (62), Expect = 0.92
Identities = 7/26 (26%), Positives = 15/26 (57%)
Query: 139 VRQRIVELAHNGVRPCDISRQLRVSH 164
+R++ L G RP +I+++L +
Sbjct: 2 IRRQARTLYWQGYRPAEIAQELGLKA 27
>gnl|CDD|238749 cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain;
equivalent to the I-domain of integrins. This domain
has a variety of functions including: intermolecular
adhesion, cell migration, signalling, transcription, and
DNA repair. In integrins these domains form heterodimers
while in vWF it forms homodimers and multimers. There
are different interaction surfaces of this domain as
seen by its complexes with collagen with either integrin
or human vWFA. In integrins collagen binding occurs via
the metal ion-dependent adhesion site (MIDAS) and
involves three surface loops located on the upper
surface of the molecule. In human vWFA, collagen binding
is thought to occur on the bottom of the molecule and
does not involve the vestigial MIDAS motif.
Length = 164
Score = 29.1 bits (66), Expect = 0.97
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 108 VVRQ-RIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRP 153
V AS S GV ++ V +G+ D V + VEL G+
Sbjct: 88 VRENLFTEASGSREGVPKVLVVITDGKS-QDDVEEPAVELKQAGIEV 133
>gnl|CDD|206107 pfam13936, HTH_38, Helix-turn-helix domain. This helix-turn-helix
domain is often found in transferases and is likely to
be DNA-binding.
Length = 44
Score = 26.2 bits (59), Expect = 1.6
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 140 RQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
R+ I L G+ +I+R+L S +S+ L R
Sbjct: 10 REEIEALLKEGLSLREIARRLGRSPSTISRELKR 43
>gnl|CDD|191937 pfam08069, Ribosomal_S13_N, Ribosomal S13/S15 N-terminal domain.
This domain is found at the N-terminus of ribosomal S13
and S15 proteins. This domain is also identified as
NUC021.
Length = 60
Score = 26.8 bits (60), Expect = 1.8
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165
P+ V + IV+LA G+ P I LR +G
Sbjct: 30 PEEVEELIVKLAKKGLTPSQIGVILRDQYG 59
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 28.5 bits (64), Expect = 2.3
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 76 SSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASR 117
+ +N+Y+ +V GG +V LPDV +IVASR
Sbjct: 206 TGVNKYVYFV------CTSPGGPWVR---LPDVTPAQIVASR 238
>gnl|CDD|216864 pfam02072, Orexin, Prepro-orexin.
Length = 129
Score = 27.7 bits (61), Expect = 2.4
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 100 VNGRPLPDVVRQRIVASRS----HGGVNQLGGVFVNG--RPLPDVVRQRIVELAH 148
+PLPD RQ+ + R HG N G+ G RP P ++ R+ L
Sbjct: 30 GGAQPLPDCCRQKTCSCRLYELLHGAGNHAAGILTLGKRRPGPPGLQGRLQRLLQ 84
>gnl|CDD|235078 PRK02858, PRK02858, germination protease; Provisional.
Length = 369
Score = 28.1 bits (63), Expect = 3.6
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 16 YETGSFKAGVIGGSKPKVATAPVVDAIA--SYKRENPT 51
ET G+I +KP A +DA+A S +R N T
Sbjct: 170 IETSDIIYGIIEKTKPDFVIA--IDALAARSIERVNTT 205
>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 = 25.1 bits (56), Expect = 6.7
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 155 DISRQLRVSHGCVSKILSRESNLHNYRLVREE 186
DI+R VS VS++L+ V EE
Sbjct: 2 DIARAAGVSVATVSRVLN------GKPRVSEE 27
>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 = 25.2 bits (56), Expect = 6.9
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 147 AHNGVRPCDISRQLRVSHGCVSKILSR 173
G+ +++R+L +S VS+++ R
Sbjct: 16 RAGGLTVAELARRLGLSKQTVSRLVKR 42
>gnl|CDD|225310 COG2512, COG2512, Predicted membrane-associated trancriptional
regulator [Transcription].
Length = 258
Score = 27.0 bits (60), Expect = 7.1
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 130 VNGRPLPDVVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186
VN L + ++ + + G + ++ R L +S VS+IL R L L+ +E
Sbjct: 188 VNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRR---LEKRGLIEKE 243
>gnl|CDD|219678 pfam07976, Phe_hydrox_dim, Phenol hydroxylase, C-terminal
dimerisation domain. Phenol hydroxylase acts a
homodimer, to hydroxylates phenol to catechol or similar
product. The enzyme is comprised of three domains. The
first two domains from the active site. The third
domain, this domain, is involved in forming the
dimerisation interface. The domain adopts a
thioredoxin-like fold.
Length = 169
Score = 26.4 bits (59), Expect = 7.6
Identities = 15/41 (36%), Positives = 17/41 (41%), Gaps = 5/41 (12%)
Query: 113 IVASRSHGGVNQLGGVFVNGRPLPD--VVRQ---RIVELAH 148
+VA H + L GR LP VVRQ V L H
Sbjct: 14 LVAKPEHQAKSYLATGLPPGRRLPSAKVVRQADANPVHLGH 54
>gnl|CDD|185427 PTZ00072, PTZ00072, 40S ribosomal protein S13; Provisional.
Length = 148
Score = 26.2 bits (58), Expect = 8.1
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165
V +I +LA G+ P I LR S G
Sbjct: 27 SSEVEDQICKLAKKGLTPSQIGVILRDSMG 56
>gnl|CDD|218541 pfam05292, MCD, Malonyl-CoA decarboxylase (MCD). This family
consists of several eukaryotic malonyl-CoA decarboxylase
(MLYCD) proteins. Malonyl-CoA, in addition to being an
intermediate in the de novo synthesis of fatty acids, is
an inhibitor of carnitine palmitoyltransferase I, the
enzyme that regulates the transfer of long-chain fatty
acyl-CoA into mitochondria, where they are oxidized.
After exercise, malonyl-CoA decarboxylase participates
with acetyl-CoA carboxylase in regulating the
concentration of malonyl-CoA in liver and adipose
tissue, as well as in muscle. Malonyl-CoA decarboxylase
is regulated by AMP-activated protein kinase (AMPK).
Length = 354
Score = 26.9 bits (59), Expect = 8.2
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 11/42 (26%)
Query: 101 NGRPLPDVVR---------QRI--VASRSHGGVNQLGGVFVN 131
G+ L V +R+ + RS G+ Q GG+ VN
Sbjct: 309 RGKALDSVANFHLQNGAMLERLNWMGDRSEKGIRQSGGIMVN 350
>gnl|CDD|176553 cd08612, GDPD_GDE4, Glycerophosphodiester phosphodiesterase domain
of mammalian glycerophosphodiester phosphodiesterase
GDE4 and similar proteins. This subfamily corresponds
to the glycerophosphodiester phosphodiesterase domain
(GDPD) present in mammalian GDE4 (also known as
glycerophosphodiester phosphodiesterase
domain-containing protein 1 (GDPD1)) and similar
proteins. Mammalian GDE4 is a transmembrane protein
whose cellular function has not yet been elucidated. It
is expressed widely, including in placenta, liver,
kidney, pancreas, spleen, thymus, ovary, small intestine
and peripheral blood leukocytes. It is also expressed in
the growth cones in neuroblastoma Neuro2a cells, which
suggests GDE4 may play some distinct role from other
members of the GDE family.
Length = 300
Score = 26.8 bits (60), Expect = 8.3
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 3/30 (10%)
Query: 38 VVDAIASYKRENPTMFA---WEIRDRLLAE 64
V D + YKRE+ T++ EI + E
Sbjct: 152 VSDLVRKYKREDITVWGSFNDEIVKKCHKE 181
>gnl|CDD|183535 PRK12454, PRK12454, carbamate kinase-like carbamoyl phosphate
synthetase; Reviewed.
Length = 313
Score = 26.5 bits (59), Expect = 9.1
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 13 RRYYETGSFKAGVIGGSKPKVATA 36
++YYE G FKAG +G PK+ A
Sbjct: 260 KKYYEEGHFKAGSMG---PKILAA 280
>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 = 24.5 bits (54), Expect = 9.7
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 140 RQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
R +IVEL G + +R+L +S V + + R
Sbjct: 2 RLKIVELYLEGESIREAARKLGISRRTVYRWIKR 35
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 0.140 0.424
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: 10,425,067
Number of extensions: 997809
Number of successful extensions: 905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 905
Number of HSP's successfully gapped: 38
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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: 56 (25.4 bits)