RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17455
(149 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 70.7 bits (174), Expect = 7e-17
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 22 NSLLKKETLVDLR-SAEGQYLKAHKVVLCTCSPVFEIPLFEMLLSQHNDERPILIFSETK 80
N L + L D+ + AHK VL CSP F+ + E + S
Sbjct: 2 NELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFK----ALFTGNKEVEITLEDVS--- 54
Query: 81 FNELKSMIDYMYKGEVNIAPDELNHFLKAAERLQIRGLSE 120
+ +++++++Y G++ I + ++ L A++LQI L +
Sbjct: 55 PEDFEALLEFIYTGKLEITEENVDDLLALADKLQIPALID 94
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 63.1 bits (154), Expect = 6e-14
Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 5/87 (5%)
Query: 36 AEGQYLKAHKVVLCTCSPVFEIPLFEMLLSQH-NDERPILIFSETKFNELKSMIDYMYKG 94
G+ AHK VL SP F+ + S ++ + + + +++++++Y G
Sbjct: 6 VGGKKFHAHKAVLAAHSPYFK----ALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYTG 61
Query: 95 EVNIAPDELNHFLKAAERLQIRGLSES 121
++++ + + L+ A+ LQI GL E
Sbjct: 62 KLDLPEENVEELLELADYLQIPGLVEL 88
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 36.7 bits (85), Expect = 0.002
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 42 KAHKVVLCTCSPVFEIPLFEMLLSQHNDERPILIFSETKFNELKSMIDYMYKGEVNIAPD 101
K HK++L + S F+ M + + L FNE+ I Y+Y G++NI +
Sbjct: 24 KVHKIILSSSSEYFKK----MFKNNFKENEINLNIDYDSFNEV---IKYIYTGKINITSN 76
Query: 102 ELNHFLKAAERLQI 115
+ L A L I
Sbjct: 77 NVKDILSIANYLII 90
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 30.7 bits (70), Expect = 0.24
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 88 IDYMYKGEVNIAPDELNHFLKAAERLQIRGLS 119
+DY+Y + P++L + L RGL+
Sbjct: 34 LDYVYLA-FEVPPEDLPEAVSGIRALGFRGLN 64
>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver
domain and AraC-type DNA-binding domain [Signal
transduction mechanisms].
Length = 475
Score = 29.6 bits (67), Expect = 0.58
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 77 SETKFNELKSMIDYMYKGEVNIAPDELNHFLKAAER 112
+E E DY +K + + PD+ N LK
Sbjct: 245 AEKLGFEEADYFDYRFKKYLGMTPDQYNKQLKQNIT 280
>gnl|CDD|212677 cd10235, HscC_like_NBD, Nucleotide-binding domain of Escherichia
coli HscC and similar proteins. This subfamily
includes Escherichia coli HscC (also called heat shock
cognate protein C, Hsc62, or YbeW) and the the putative
DnaK-like protein Escherichia coli ECs0689. It belongs
to the heat shock protein 70 (Hsp70) family of
chaperones that assist in protein folding and assembly
and can direct incompetent "client" proteins towards
degradation. Typically, Hsp70s have a nucleotide-binding
domain (NBD) and a substrate-binding domain (SBD). The
nucleotide sits in a deep cleft formed between the two
lobes of the NBD. The two subdomains of each lobe change
conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is
regulated by various co-chaperones: J-domain proteins
and nucleotide exchange factors (NEFs). Two genes in the
vicinity of the HscC gene code for potential
cochaperones: J-domain containing proteins, DjlB/YbeS
and DjlC/YbeV. HscC and its co-chaperone partners may
play a role in the SOS DNA damage response. HscC does
not appear to require a NEF.
Length = 339
Score = 28.6 bits (65), Expect = 1.3
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 14/75 (18%)
Query: 81 FNELKSMIDYMYK----GEVNIAPDELNHFLKAAERLQIRGLSESESTTQTAVHYPDD-- 134
F + + K + P EL L+AAER + LS+ E +V +
Sbjct: 200 FTRA--LAEAFLKKHGLDFEKLDPSELARLLRAAERAKRA-LSDQEEAE-MSVRIEGEEL 255
Query: 135 ----DEEDYSQAGTS 145
E++ +
Sbjct: 256 EYTLTREEFEEICQP 270
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 28.1 bits (63), Expect = 1.7
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 23 SLLKKETLVDLRSAEGQYLKAHKVVLCTCS 52
LKKE +S + L VV T S
Sbjct: 135 KKLKKELERLRKSIRKEILDEADVVCTTLS 164
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 27.9 bits (61), Expect = 1.7
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 61 EMLLSQHNDERPILIFSETKFNELKSMIDYMY 92
E+L++ + +RPILI S++K+ + S+ ++Y
Sbjct: 52 ELLIATRHTDRPILILSDSKY-VINSLTKWVY 82
>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Alanine Racemase. This family
includes predominantly bacterial alanine racemases (AR),
some serine racemases (SerRac), and putative
bifunctional enzymes containing N-terminal
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase (murF) and C-terminal AR domains. These proteins
are fold type III PLP-dependent enzymes that play
essential roles in peptidoglycan biosynthesis. AR
catalyzes the interconversion between L- and D-alanine,
which is an essential component of the peptidoglycan
layer of bacterial cell walls. SerRac converts L-serine
into its D-enantiomer (D-serine) for peptidoglycan
synthesis. murF catalyzes the addition of D-Ala-D-Ala to
UDPMurNAc-tripeptide, the final step in the synthesis of
the cytoplasmic precursor of bacterial cell wall
peptidoglycan. Members of this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain. They exist as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. AR and other
members of this family require dimer formation and the
presence of the PLP cofactor for catalytic activity.
Fungal ARs and eukaryotic serine racemases, which are
fold types I and II PLP-dependent enzymes respectively,
are excluded from this family.
Length = 367
Score = 27.5 bits (62), Expect = 2.9
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 11/58 (18%)
Query: 64 LSQHNDERPILIFSETKFNELKSMIDYMYKGEVNIAP-----DELNHFLKAAERLQIR 116
L + PIL+ T E + I+Y ++ P ++ AA RL
Sbjct: 67 LREAGITAPILVLGGTPPEEAEEAIEY------DLTPTVSSLEQAEALSAAAARLGKT 118
>gnl|CDD|149523 pfam08501, Shikimate_dh_N, Shikimate dehydrogenase substrate
binding domain. This domain is the substrate binding
domain of shikimate dehydrogenase.
Length = 83
Score = 26.0 bits (58), Expect = 3.9
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 88 IDYMYKGEVNIAPDELNHFLKAAERLQIRGLS 119
++ +Y + PD L F++ L RGL+
Sbjct: 24 LNGVYV-AFEVPPDNLPEFVEGLRALGFRGLN 54
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 26.4 bits (59), Expect = 5.0
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 4/49 (8%)
Query: 6 QEFCLRANQETMISLVN----SLLKKETLVDLRSAEGQYLKAHKVVLCT 50
E RA + + L + + A+G L+A VVL T
Sbjct: 102 SELLARAPAGVTVRVHRAEVVDLRPRGGGYTVTLADGATLRADAVVLAT 150
>gnl|CDD|215326 PLN02606, PLN02606, palmitoyl-protein thioesterase.
Length = 306
Score = 26.1 bits (57), Expect = 7.7
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 64 LSQHNDERPILIFS--ETKFNELKSMIDYMYKGEVNIAPDELNHFLKAAERLQIRGLSES 121
L + N+ERP + +F L +++ M++G+ + P E + F + LS
Sbjct: 188 LPKLNNERPGERNPTFKDRFTSLHNLVLVMFQGDTVLIPRETSWFGYYPDGASTPLLSPQ 247
Query: 122 ESTTQT 127
+ T
Sbjct: 248 STKLYT 253
>gnl|CDD|240326 PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional.
Length = 158
Score = 25.8 bits (57), Expect = 8.0
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 40 YLKAHKVVLCTCSPVFEI 57
Y K HK + CSP F++
Sbjct: 100 YEKRHKNIPVHCSPCFDV 117
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 26.1 bits (58), Expect = 10.0
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 6 QEFCLRANQETMISLVNSLLKKETLVDLRSAEGQYLKAHKVVLCT 50
L N E + SL + L A G+ + A VVL
Sbjct: 147 IRLTLHFNTE-----ITSLERDGEGWQLLDANGEVIAASVVVLAN 186
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
0.315 0.130 0.361
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,148,775
Number of extensions: 622796
Number of successful extensions: 601
Number of sequences better than 10.0: 1
Number of HSP's gapped: 599
Number of HSP's successfully gapped: 29
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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 (21.5 bits)
S2: 54 (24.6 bits)