RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1898
(230 letters)
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain.
Length = 125
Score = 227 bits (579), Expect = 8e-77
Identities = 97/123 (78%), Positives = 111/123 (90%), Gaps = 1/123 (0%)
Query: 86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
VNQLGGVF+NGRPLPNHIR KIVE+A +GVRPC ISRQLRVSHGCVSKIL RYQETGSI
Sbjct: 4 RVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSI 63
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
RPGVIGGSKP+VATP+V K+I EYK+ NPGIF+WEIRDRL+ +G+CD ++ PSVSSISR
Sbjct: 64 RPGVIGGSKPKVATPEVVKKIAEYKRENPGIFAWEIRDRLLA-EGVCDNDNVPSVSSISR 122
Query: 206 LLR 208
+LR
Sbjct: 123 ILR 125
>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
Length = 128
Score = 220 bits (563), Expect = 3e-74
Identities = 94/124 (75%), Positives = 112/124 (90%), Gaps = 1/124 (0%)
Query: 86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
GVNQLGGVF+NGRPLP+ IR +IVE+A +G+RPC ISRQLRVSHGCVSKILNRY ETGSI
Sbjct: 4 GVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSI 63
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
RPG IGGSKPRVATP+V K+IE YK+ NPG+F+WEIRDRL+ Q+G+CDK++ PSVSSI+R
Sbjct: 64 RPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLL-QEGVCDKSNVPSVSSINR 122
Query: 206 LLRG 209
+LR
Sbjct: 123 ILRN 126
>gnl|CDD|128645 smart00351, PAX, Paired Box domain.
Length = 125
Score = 213 bits (545), Expect = 1e-71
Identities = 90/123 (73%), Positives = 106/123 (86%), Gaps = 1/123 (0%)
Query: 86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
GVNQLGGVF+NGRPLP+ R +IVE+A GVRPC ISRQL VSHGCVSKIL RY ETGSI
Sbjct: 4 GVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSI 63
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
RPG IGGSKP+VATP V K+I +YK+ NPGIF+WEIRDRL+ +G+CDK++ PSVSSI+R
Sbjct: 64 RPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLL-SEGVCDKDNVPSVSSINR 122
Query: 206 LLR 208
+LR
Sbjct: 123 ILR 125
>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 = 40.4 bits (95), Expect = 8e-05
Identities = 26/111 (23%), Positives = 48/111 (43%), Gaps = 12/111 (10%)
Query: 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRVATPDV 162
R + + + A GV I+R L +S V + L R+ E G +++ G +P+
Sbjct: 1 RAQALLLLAEGVSVAQIARLLGLSRRTVYRWLKRFNEGGLAALKDRPRSGRPRNRLSPEQ 60
Query: 163 EKRIEEYKKTNP--GIFSWE---IRDRLVKQDGICDKNSAPSVSSISRLLR 208
E + + P G W + + L ++ G+ S S++ RLL+
Sbjct: 61 EAALVALAREKPPEGFARWTLELLAELLERRFGV-----TVSRSTVRRLLK 106
>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain.
Length = 50
Score = 38.0 bits (89), Expect = 1e-04
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143
R +I+ + A G+ I+ L VS V + L RY+E G
Sbjct: 6 RRAEILLLLAEGLSVKEIAELLGVSRRTVYRWLKRYREGG 45
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 60 IRLKIVEMAAAGVRPCVISRQLRVSH 85
R +I+ + A G+ I+ L VS
Sbjct: 6 RRAEILLLLAEGLSVKEIAELLGVSR 31
>gnl|CDD|222226 pfam13565, HTH_32, Homeodomain-like domain.
Length = 74
Score = 38.1 bits (89), Expect = 2e-04
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 132 VSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIF--SWEIRDRLVKQD 189
V + L RY+E G+ G P+ + I P ++L +
Sbjct: 2 VYRWLKRYREEGAAGLVHRPGRPSNHRYPEELRAIVLTLIREPYADFGPTLAAEKLAELH 61
Query: 190 GICDKNSAPSVSSISRLL 207
G+ S ++ R L
Sbjct: 62 GLK-----ISRETLRRWL 74
>gnl|CDD|225949 COG3415, COG3415, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 138
Score = 33.5 bits (77), Expect = 0.034
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 121 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 168
+++ VS V + + RY+ETG P +PR + + + + E
Sbjct: 27 AAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLE 74
>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 = 31.4 bits (72), Expect = 0.036
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143
RLKIVE+ G +R+L +S V + + RY+E G
Sbjct: 2 RLKIVELYLEGESIREAARKLGISRRTVYRWIKRYEEGG 40
>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 = 30.3 bits (69), Expect = 0.16
Identities = 11/51 (21%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 97 GRPLPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
+ L + RL+I+ + + ++ +L +S VS+ L + +E G +
Sbjct: 1 LKALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51
>gnl|CDD|172498 PRK13997, PRK13997, potassium-transporting ATPase subunit C;
Provisional.
Length = 193
Score = 30.7 bits (69), Expect = 0.38
Identities = 30/87 (34%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 126 RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRL 185
R HG VS I + + +GS S P + VEK IEE+KK NP + E+ L
Sbjct: 68 RYFHGRVSSIEYKAEASGS---NNYAPSNPDLEK-RVEKSIEEWKKQNPSVPVTEVPIDL 123
Query: 186 VKQDG------ICDKNSAPSVSSISRL 206
V G I K ++ V IS+L
Sbjct: 124 VTNSGSGLDPDISPKAASVQVERISKL 150
>gnl|CDD|113682 pfam04918, DltD_M, DltD central region. DltD is and integral
membrane protein involved in the biosynthesis of
D-alanyl-lipoteichoic acid. This is important in
controlling the net ionic charge in lipoteichoic acid
(LTA). This family is found in bacteria of the
Bacillus/Clostridium group. DltD binds Dcp and ligates
it with D-alanine. DltD does not ligate acyl carrier
protein (ACP) with D-alanine. It also has thioesterase
activity for mischarged D-alanyl-acyl carrier protein
(ACP). DltD is thought to be responsible for
discriminating between Dcp involved in the D-alanylation
of LTA, and ACP involved in fatty acid biosynthesis.
This family consists of the central region of DltD.
Length = 163
Score = 29.6 bits (67), Expect = 0.80
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 163 EKRIEEYKKTNPGIFSWEIRDRLVKQDG 190
+KR+ +Y K P FS++ ++L K+DG
Sbjct: 129 QKRVSKYLKILPKDFSYDELNQLAKEDG 156
>gnl|CDD|226475 COG3966, DltD, Protein involved in D-alanine esterification of
lipoteichoic acid and wall teichoic acid (D-alanine
transfer protein) [Cell envelope biogenesis, outer
membrane].
Length = 415
Score = 30.1 bits (68), Expect = 0.88
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAP 198
K I++ K P FS++ ++L + G + P
Sbjct: 225 LKHIKKALKDLPDQFSYKELEKLAVEIGKKSTTNNP 260
>gnl|CDD|234108 TIGR03104, trio_amidotrans, asparagine synthase family
amidotransferase. Members of this protein family are
closely related to several isoforms of asparagine
synthetase (glutamine amidotransferase) and typically
have been given this name in genome annotation to date.
Each is part of a conserved three-gene cassette
sparsely distributed across at least twenty different
species known so far, including alpha, beta, and gamma
Proteobacteria, Mycobacterium, and Prosthecochloris,
which is a member of the Chlorobi. The other two
members of the cassette are a probable protease and a
member of the GNAT family of acetyltransferases.
Length = 589
Score = 29.7 bits (67), Expect = 1.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 47 GGVFINGRPLPNHIRLKIVEMAAAGVRPCV 76
GGV G H RLKI++++ A +P V
Sbjct: 35 GGVHAQGPVALGHRRLKIIDLSEASQQPMV 64
Score = 29.7 bits (67), Expect = 1.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 91 GGVFINGRPLPNHIRLKIVEMAAAGVRPCV 120
GGV G H RLKI++++ A +P V
Sbjct: 35 GGVHAQGPVALGHRRLKIIDLSEASQQPMV 64
>gnl|CDD|239700 cd03730, SOCS_ASB14, SOCS (suppressors of cytokine signaling) box
of ASB14-like proteins. ASB family members have a
C-terminal SOCS box and an N-terminal ankyrin-related
sequence. The general function of the SOCS box is the
recruitment of the ubiquitin-transferase system. The
SOCS box interacts with Elongins B and C, Cullin-5 or
Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing
proteins probably function as E3 ubiquitin ligases and
mediate the degradation of proteins associated through
their N-terminal regions.
Length = 57
Score = 26.7 bits (59), Expect = 2.1
Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 11/49 (22%)
Query: 15 NGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLK 63
N R L + RLKI C GR+ VF++ PLPN RLK
Sbjct: 2 NPRSLKHLCRLKIRA---------CMGRLRLRCPVFMSFLPLPN--RLK 39
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.3 bits (64), Expect = 3.5
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 26/79 (32%)
Query: 13 FINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPN--HIRLKIVE---- 66
F G+ + IR ++++ ++ QLG +I G+P + + L+ VE
Sbjct: 88 FKAGQHIRQQIRQQVLD------------KLQQLGPAWIQGKPAGSWATLVLEQVEDMHD 135
Query: 67 --------MAAAGVRPCVI 77
MA A + P +I
Sbjct: 136 FYARYLPQMALAVLVPLLI 154
>gnl|CDD|217758 pfam03843, Slp, Outer membrane lipoprotein Slp family.
Length = 160
Score = 27.2 bits (61), Expect = 4.5
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 31 AAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIV 65
+ G+ + GGV + L + RL+IV
Sbjct: 24 QVKAAPDAYVGQEVRWGGVIVEVENLKDQTRLEIV 58
>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 = 5.4
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 121 ISRQLRVSHGCVSKILNRYQETGSIR 146
++R+L +S VS+++ R +E G +
Sbjct: 25 LARRLGLSKQTVSRLVKRLEEKGLVE 50
>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 = 24.7 bits (55), Expect = 8.6
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 16/48 (33%)
Query: 121 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 168
I+R VS VS++LN KPRV+ + +R+
Sbjct: 3 IARAAGVSVATVSRVLNG---------------KPRVS-EETRERVLA 34
>gnl|CDD|184154 PRK13573, PRK13573, anthranilate synthase component I; Provisional.
Length = 503
Score = 27.0 bits (60), Expect = 9.3
Identities = 11/24 (45%), Positives = 18/24 (75%), Gaps = 2/24 (8%)
Query: 144 SIRPGVIGGSKPRVATPDVEKRIE 167
+IRP I G++PR ATP+ ++ +E
Sbjct: 309 TIRP--IAGTRPRGATPEEDRALE 330
>gnl|CDD|184445 PRK13995, PRK13995, potassium-transporting ATPase subunit C;
Provisional.
Length = 203
Score = 26.7 bits (59), Expect = 9.8
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 15/95 (15%)
Query: 126 RVSHGCVSKI-LNRY--QETGSIR-PGVIGGSKPRVAT-PDVEKR----IEEYKKTNPGI 176
R G VS + N Y ++ G+ GV GS+ T P++ R I+++ KTNP +
Sbjct: 63 RFFKGRVSAVNYNTYTKEDKGNGNYGGVSSGSQNYAPTNPELHDRVQKDIDKFLKTNPTV 122
Query: 177 FSWEIRDRLVKQDG------ICDKNSAPSVSSISR 205
+I L+ G I K++A + ++S+
Sbjct: 123 KKEDIPTDLLTASGSGLDPHISPKSAAIQIPAVSK 157
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 0.419
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: 12,100,460
Number of extensions: 1168454
Number of successful extensions: 1080
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1077
Number of HSP's successfully gapped: 42
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
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: 57 (25.7 bits)