RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy333
(70 letters)
>gnl|CDD|215366 PLN02681, PLN02681, proline dehydrogenase.
Length = 455
Score = 76.3 bits (188), Expect = 3e-18
Identities = 29/53 (54%), Positives = 41/53 (77%)
Query: 3 GQAGYSAYKYIPYGPVNEVLPYLSRRATENKGVLEKISKEKKLLRQEILRRIK 55
G AG+ KY+PYGPV EV+PYL RRA EN+G+L + +++LLR+E+ RR+K
Sbjct: 399 GNAGFRVSKYLPYGPVEEVIPYLLRRAEENRGLLSGSAIDRQLLRKELKRRLK 451
>gnl|CDD|216609 pfam01619, Pro_dh, Proline dehydrogenase.
Length = 341
Score = 59.3 bits (144), Expect = 3e-12
Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 3 GQAGYSAYKYIPYGPVNEVLPYLSRRATENKGVLEKISKEKKLL 46
G+AGY+ KY PYGPV E+L YL RR EN +++E+ L
Sbjct: 298 GKAGYNVRKYAPYGPVEELLAYLVRRLLENGANSSFVNRERDLK 341
>gnl|CDD|151248 pfam10798, YmgB, Biofilm development protein YmgB/AriR. YmgB is
part of the three gene cluster ymgABC which has a role
in biofilm development and stability. YmgB represses
biofilm formation in rich medium containing glucose,
decreases cellular motility and also protects the cell
from acid which indicates that YmgB has an important
function in acid-resistance. YmgB binds as a dimer to
genes which are important for biofilm formation via a
ligand. Due to its important function in acid
resistance it is also known as AriR (regulator of acid
resistance influenced by indole).
Length = 60
Score = 28.1 bits (63), Expect = 0.094
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 18 VNEVLPYLSRRATENKGV----LEKISKEKKLLRQEILRRIKSGKLFYTP 63
V E+L S NK + + K+ E ++R ++ R+ + TP
Sbjct: 11 VTELL--QSGGHVSNKDIILKLIHKLETESDVVRADVYRKTLEIVVRKTP 58
>gnl|CDD|221448 pfam12161, HsdM_N, HsdM N-terminal domain. This domain is found
at the N-terminus of the methylase subunit of Type I
DNA methyltransferases. This domain family is found in
bacteria and archaea, and is typically between 123 and
138 amino acids in length. The family is found in
association with pfam02384. Mutations in this region of
EcoKI methyltransferase abolish the normally strong
preference of this system for methylating
hemimethylated substrate. The structure of this domain
has been shown to be all alpha-helical.
Length = 96
Score = 27.9 bits (63), Expect = 0.19
Identities = 10/37 (27%), Positives = 21/37 (56%)
Query: 18 VNEVLPYLSRRATENKGVLEKISKEKKLLRQEILRRI 54
+N+ P + + KGV K + KLL+ ++L+++
Sbjct: 56 LNDAFPGIEELNPDLKGVFMKDAFITKLLKPKLLKKV 92
>gnl|CDD|167581 PRK03670, PRK03670, competence damage-inducible protein A;
Provisional.
Length = 252
Score = 27.8 bits (62), Expect = 0.36
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 19 NEVLPYLSRRATENKGVLEKISKEKKL--LRQEILRRIKSGKLFYTPKG 65
EVLP L R K L +I+ E KL + +E L R K+ +PKG
Sbjct: 170 KEVLPRLGERKFVQKKFLAEITDESKLAPILEEALERFNV-KIHSSPKG 217
>gnl|CDD|237017 PRK11904, PRK11904, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1038
Score = 26.7 bits (60), Expect = 0.93
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 12 YIPYGPVNEVLPYLSRRATEN 32
Y P G ++LPYL RR EN
Sbjct: 452 YAPVGSHKDLLPYLVRRLLEN 472
>gnl|CDD|197217 cd09118, PLDc_yjhR_C_like, C-terminal domain of Escherichia coli
uncharacterized protein yjhR and similar proteins.
C-terminal domain of Escherichia coli uncharacterized
protein yjhR, encoded by the o338 gene, and similar
proteins. Although the biological function of yjhR
remains unknown, it shows sequence similarity to the
C-terminal portions of superfamily I DNA and RNA
helicases, which are ubiquitous enzymes mediating
ATP-dependent unwinding of DNA and RNA duplexes, and
play essential roles in gene replication and
expression. Moreover, The C-termini of yjhR and similar
proteins contain one HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The PLDc-like
domain of yjhR is similar to bacterial endonucleases,
Nuc and BfiI, both of which have only one copy of the
HKD motif per chain. They function as homodimers, with
a single active site at the dimer interface containing
the HKD motifs from both subunits. They utilize a
two-step mechanism to cleave phosphodiester bonds. Upon
substrate binding, the bond is first attacked by a
histidine residue from one HKD motif to form a covalent
phosphohistidine intermediate, which is then hydrolyzed
by water with the aid of a second histidine residue
from the other HKD motif in the opposite subunit.
Length = 144
Score = 25.7 bits (57), Expect = 1.6
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 21 VLPYLSRRATENKGVLEKISK 41
V P++S A E G+LE I +
Sbjct: 20 VSPWISLDALEADGLLEAIRE 40
>gnl|CDD|216854 pfam02033, RBFA, Ribosome-binding factor A.
Length = 104
Score = 25.5 bits (57), Expect = 1.7
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 31 ENKGVLEKISKEKKLLRQEILRRIKSGKLFYTPK 64
E + L+ ++K +R E+ +R+ +L YTP+
Sbjct: 55 EKEETLKALNKAAGFIRSELAKRL---RLRYTPE 85
>gnl|CDD|223927 COG0858, RbfA, Ribosome-binding factor A [Translation, ribosomal
structure and biogenesis].
Length = 118
Score = 25.7 bits (57), Expect = 1.7
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 25 LSRRATENKGVLEKISKEKKLLRQEILRRIKSGKLFYTPKGHY 67
L + +L ++K K +R E+ +R+ +L TP+ H+
Sbjct: 55 LGDEESSKAEILAALNKAKGFIRSELGKRL---RLRKTPELHF 94
>gnl|CDD|217987 pfam04250, DUF429, Protein of unknown function (DUF429).
Length = 202
Score = 25.9 bits (57), Expect = 1.9
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 16 GPVNEVLPYLSRRATENKGVLEKISKEKKLLRQEILRRI 54
V E P S +A V K +KE + R+ +L R+
Sbjct: 112 LEVIETHPEASFKALGGSPVASKKTKEGRAERRALLARL 150
>gnl|CDD|215477 PLN02882, PLN02882, aminoacyl-tRNA ligase.
Length = 1159
Score = 25.5 bits (56), Expect = 2.3
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 17 PVNEVLPYLSRRATENKGVLEK--------ISKEKKLLRQE-ILRRIKSGKL 59
P N+ L Y S RA N VL K ++KE K + Q+ IL K+G++
Sbjct: 891 PCNDPLKYASLRAEPNFSVLGKRLGKSMGLVAKEVKAMSQDDILEFEKAGEV 942
>gnl|CDD|218482 pfam05178, Kri1, KRI1-like family. The yeast member of this
family (Kri1p) is found to be required for 40S ribosome
biogenesis in the nucleolus.
Length = 99
Score = 24.9 bits (55), Expect = 2.4
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 27 RRATENKGVLEKISKEKKLLRQEILRRIK 55
R+ E E++ + K L R+EI +++
Sbjct: 3 RKEEEKAQREEELKRLKNLKREEIEEKLE 31
>gnl|CDD|226683 COG4230, COG4230, Delta 1-pyrroline-5-carboxylate dehydrogenase
[Energy production and conversion].
Length = 769
Score = 25.4 bits (56), Expect = 2.7
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 12 YIPYGPVNEVLPYLSRRATEN 32
Y P G +L YL RR EN
Sbjct: 13 YAPVGTHETLLAYLVRRLLEN 33
>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA
binding. This is the C-terminal conserved coiled coil
region of a family of TATA element modulatory factor 1
proteins conserved in eukaryotes. The proteins bind to
the TATA element of some RNA polymerase II promoters
and repress their activity. by competing with the
binding of TATA binding protein. TMF1_TATA_bd is the
most conserved part of the TMFs. TMFs are
evolutionarily conserved golgins that bind Rab6, a
ubiquitous ras-like GTP-binding Golgi protein, and
contribute to Golgi organisation in animal and plant
cells. The Rab6-binding domain appears to be the same
region as this C-terminal family.
Length = 121
Score = 24.8 bits (55), Expect = 2.9
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 36 LEKISKEKKLLRQEILR 52
L ++ E+ RQEI++
Sbjct: 40 LARLEAERDEARQEIVK 56
>gnl|CDD|234787 PRK00521, rbfA, ribosome-binding factor A; Validated.
Length = 120
Score = 25.1 bits (56), Expect = 2.9
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 31 ENKGVLEKISKEKKLLRQEILRRIKSGKLFYTP 63
+ + L + K LR E+ +R+ +L Y P
Sbjct: 61 DKEEALAALKKAAGFLRSELGKRL---RLRYVP 90
>gnl|CDD|100080 cd06159, S2P-M50_PDZ_Arch, Uncharacterized Archaeal homologs of
Site-2 protease (S2P), zinc metalloproteases (MEROPS
family M50) which cleave transmembrane domains of
substrate proteins, regulating intramembrane
proteolysis (RIP) of diverse signal transduction
mechanisms. Members of the S2P/M50 family of RIP
proteases use proteolytic activity within the membrane
to transfer information across membranes to integrate
gene expression with physiologic stresses occurring in
another cellular compartment. In eukaryotic cells they
regulate such processes as sterol and lipid metabolism,
and endoplasmic reticulum stress responses. In
prokaryotes they regulate such processes as
sporulation, cell division, stress response, and cell
differentiation. This group appears to be limited to
Archaeal S2P/M50s homologs with additional putative
N-terminal transmembrane spanning regions, relative to
the core protein, and either one or two PDZ domains
present.
Length = 263
Score = 25.0 bits (55), Expect = 3.5
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 23 PYLSRRATENKGVLEKISKEKKLLR 47
P+L R + +G ++K+++ K+ R
Sbjct: 32 PFLMLRTKKGRGFIDKLARPKRFWR 56
>gnl|CDD|213811 TIGR03427, ABC_peri_uca, ABC transporter periplasmic binding
protein, urea carboxylase region. Members of this
family are ABC transporter periplasmic binding proteins
associated with the urea carboxylase/allophanate
hydrolase pathway, an alternative to urease for urea
degradation. The protein is restricted to bacteria with
the pathway, with its gene close to the urea carboxylase
and allophanate hydrolase genes. The substrate for this
transporter therefore is likely to be urea or a compound
from which urea is easily derived [Transport and binding
proteins, Unknown substrate].
Length = 328
Score = 25.1 bits (55), Expect = 3.6
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 20 EVLPYLSRRATENKGVLEKISKEKKLLRQEILRRIKSGKLFYTPK 64
E + +S K LE ++K ++K+ K+FYTPK
Sbjct: 213 ETMALMSAGDAAGKAALEAMAKASGTDLAGYKAQLKTTKMFYTPK 257
>gnl|CDD|131313 TIGR02260, benz_CoA_red_B, benzoyl-CoA reductase, bcr type, subunit
B. This model describes B, or beta, subunit of the bcr
type of benzoyl-CoA reductase, a 4-subunit enzyme. Many
aromatic compounds are metabolized by way of
benzoyl-CoA.
Length = 413
Score = 24.6 bits (53), Expect = 5.5
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 44 KLLRQEILRRIKSGKLFYTPKG 65
LR EI +RI GK TP G
Sbjct: 240 GFLRAEIEQRIAEGKGPITPDG 261
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 23.9 bits (52), Expect = 8.5
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 18 VNEVLPYLSRRATENKGVLEKISKEKKLLRQEI 50
+ E YL + + + LEKIS +K L ++
Sbjct: 232 LPETKQYLKKLSQDLSKALEKISSREKHLNNQL 264
>gnl|CDD|200557 cd10931, CE4_u7, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 224
Score = 23.7 bits (52), Expect = 8.9
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 36 LEKISKEKKLLRQEILRRIKSGKLFY 61
EK+ KEK+ L + + R + G+ Y
Sbjct: 80 PEKLKKEKERLEKILGRPVTGGRQHY 105
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
0.316 0.137 0.394
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,684,263
Number of extensions: 277814
Number of successful extensions: 398
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 25
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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: 53 (24.1 bits)