RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3020
(150 letters)
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 46.5 bits (111), Expect = 6e-08
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 104 LLKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAFAK 148
LK+ GNA + ++ EAIEAY +A++LD N + N + A+ K
Sbjct: 5 ALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLK 49
Score = 28.0 bits (63), Expect = 0.48
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNN 30
L LG Y E+I YE+ L+LDP+N
Sbjct: 12 ALFKLGDYDEAIEAYEKALELDPDN 36
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 42.4 bits (100), Expect = 5e-06
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 104 LLKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAFAK 148
L + GN + ++ EA+E Y +A++LD N + N +AA+ K
Sbjct: 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYK 46
Score = 29.3 bits (66), Expect = 0.34
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 102 ISLLKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAFAK 148
+ A + ++EA+E Y +A++LD N + N A+ K
Sbjct: 34 ADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYK 80
Score = 27.7 bits (62), Expect = 1.2
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNN 30
LG+Y+E++ YE+ L+LDP+N
Sbjct: 43 AYYKLGKYEEALEDYEKALELDPDN 67
Score = 26.6 bits (59), Expect = 2.7
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 102 ISLLKDKGNAALQANNFKEAIEAYSEAIKLD 132
+ G A + ++EA+EAY +A++LD
Sbjct: 68 AKAYYNLGLAYYKLGKYEEALEAYEKALELD 98
Score = 26.6 bits (59), Expect = 3.3
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPN 29
LG+Y+E++ YE+ L+LDPN
Sbjct: 77 AYYKLGKYEEALEAYEKALELDPN 100
Score = 25.8 bits (57), Expect = 5.8
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNNEQ 32
LG Y E++ YE+ L+LDP+N
Sbjct: 9 LYYKLGDYDEALEYYEKALELDPDNAD 35
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 35.5 bits (83), Expect = 5e-04
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 105 LKDKGNAALQANNFKEAIEAYSEAIKLDGTN 135
L + GNA L+ + EA+E Y +A++L+ N
Sbjct: 4 LYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
Score = 30.5 bits (70), Expect = 0.031
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNN 30
LG+Y E++ YE+ L+L+PNN
Sbjct: 10 AYLKLGKYDEALEYYEKALELNPNN 34
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 34.7 bits (81), Expect = 8e-04
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 105 LKDKGNAALQANNFKEAIEAYSEAIKLDGTN 135
L + GNA L+ ++ EA+E Y +A++LD N
Sbjct: 4 LYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
Score = 30.1 bits (69), Expect = 0.040
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNN 30
LG Y E++ YE+ L+LDPNN
Sbjct: 10 AYLKLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 34.0 bits (79), Expect = 0.001
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 104 LLKDKGNAALQANNFKEAIEAYSEAIKLDGTN 135
L + G A + +++EA+EAY +A++LD N
Sbjct: 3 ALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
Score = 29.8 bits (68), Expect = 0.051
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 6 CLSYLGRYKESISTYEEGLKLDPNN 30
LG Y+E++ YE+ L+LDPNN
Sbjct: 10 AYYKLGDYEEALEAYEKALELDPNN 34
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 32.7 bits (74), Expect = 0.054
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 105 LKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAF 146
LK+KGN A + +F +AI+ YS+AI+ + + +SNR+A
Sbjct: 130 LKEKGNKAYRNKDFNKAIKLYSKAIECK-PDPVYYSNRAACH 170
>gnl|CDD|215568 PLN03088, PLN03088, SGT1, suppressor of G2 allele of SKP1;
Provisional.
Length = 356
Score = 31.7 bits (72), Expect = 0.12
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 103 SLLKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAFAK 148
L+DK A ++F A++ Y++AI LD N L+++R+ A K
Sbjct: 3 KDLEDKAKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIK 48
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 31.6 bits (72), Expect = 0.13
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 83 VQMIKEIQKDPSLMTLEAKISLLK--------DKGNAALQANNFKEAIEAYSEAIKLDGT 134
Q K + DP + SLLK +G+AAL+ANN +A Y +A ++D T
Sbjct: 324 AQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVDNT 383
Query: 135 N 135
+
Sbjct: 384 D 384
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 29.2 bits (66), Expect = 0.18
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 107 DKGNAALQANNFKEAIEAYSEAIKLD 132
AAL+A ++ EA+ A A+
Sbjct: 2 ALARAALRAGDYDEALAALEAALARY 27
Score = 26.5 bits (59), Expect = 1.9
Identities = 8/31 (25%), Positives = 11/31 (35%)
Query: 105 LKDKGNAALQANNFKEAIEAYSEAIKLDGTN 135
L G A L+ EA A+ D +
Sbjct: 34 LLLLGEALLRQGRLAEAAALLRAALAADPDD 64
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 30.6 bits (69), Expect = 0.27
Identities = 21/110 (19%), Positives = 42/110 (38%), Gaps = 18/110 (16%)
Query: 21 EEGLKLDPNNEQMKEAIKDVRNQEMNDMNRGDPFANLFSDPNIFVQLQLDPRTKPFLSDP 80
EE K + ++ M + + + ++ N+ A PN +LS
Sbjct: 493 EEFSKANSQDQLMHPVLMEKIEKLKDEFNKRLSRA-----PN-------------YLSLK 534
Query: 81 SYVQMIKEIQKDPSLMTLEAKISLLKDKGNAALQANNFKEAIEAYSEAIK 130
+ M+ E + +L ++K LK + N + + I+ EA+K
Sbjct: 535 YKLDMLNEFSRAKALSEKKSKAEKLKAEINKKFKEVMDRPEIKEKMEALK 584
>gnl|CDD|226687 COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 287
Score = 30.4 bits (69), Expect = 0.30
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 109 GNAALQANNFKEAIEAYSEAIKLDGTN 135
G A + +A+ AY A++L G N
Sbjct: 163 GRAYMALGRASDALLAYRNALRLAGDN 189
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 27.4 bits (62), Expect = 0.44
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 5 SCLSYLGRYKESISTYEEGLKLDPNN 30
LG Y+E+ YE+ L+LDPNN
Sbjct: 9 QIYLQLGDYEEAKEYYEKALELDPNN 34
Score = 27.1 bits (61), Expect = 0.64
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 108 KGNAALQANNFKEAIEAYSEAIKLDGTN 135
G LQ +++EA E Y +A++LD N
Sbjct: 7 LGQIYLQLGDYEEAKEYYEKALELDPNN 34
>gnl|CDD|215333 PLN02618, PLN02618, tryptophan synthase, beta chain.
Length = 410
Score = 27.8 bits (62), Expect = 2.3
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 101 KISLLKDKGNAALQANNFKEAIEAYSEAIKLDG------TNHIL 138
+ S LKD G A + +EA+EA+ +L+G T+H L
Sbjct: 328 EHSFLKDTGRAEYYSVTDEEALEAFQRLSRLEGIIPALETSHAL 371
>gnl|CDD|227343 COG5010, TadD, Flp pilus assembly protein TadD, contains TPR
repeats [Intracellular trafficking and secretion].
Length = 257
Score = 27.4 bits (61), Expect = 2.5
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 102 ISLLKDKGNAALQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAFAKA 149
LL +G ++ NF EA+ +A +L T+ ++ AA +
Sbjct: 100 RELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQL 147
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 27.6 bits (62), Expect = 3.0
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 109 GNAALQANNFKEAIEAYSEAIKLDG 133
G+AAL N K A EAY +A D
Sbjct: 340 GDAALSQGNIKLAEEAYQKAKDFDK 364
>gnl|CDD|223227 COG0149, TpiA, Triosephosphate isomerase [Carbohydrate transport
and metabolism].
Length = 251
Score = 27.2 bits (61), Expect = 3.4
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 109 GNAALQANNFKEAIEAYSEAI 129
G A+L+A++F +EA ++A
Sbjct: 231 GGASLKADDFLAILEALAKAK 251
>gnl|CDD|133033 cd04190, Chitin_synth_C, C-terminal domain of Chitin Synthase
catalyzes the incorporation of GlcNAc from substrate
UDP-GlcNAc into chitin. Chitin synthase, also called
UDP-N-acetyl-D-glucosamine:chitin
4-beta-N-acetylglucosaminyltransferase, catalyzes the
incorporation of GlcNAc from substrate UDP-GlcNAc into
chitin, which is a linear homopolymer of GlcNAc residues
formed by covalent beta-1,4 linkages. Chitin is an
important component of the cell wall of fungi and
bacteria and it is synthesized on the cytoplasmic
surface of the cell membrane by membrane bound chitin
synthases. Studies with fungi have revealed that most of
them contain more than one chitin synthase gene. At
least five subclasses of chitin synthases have been
identified.
Length = 244
Score = 26.9 bits (60), Expect = 3.8
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 57 LFSDPNIFVQLQLDPRTKPFLSDPSYVQMIKEIQKDPSLMTLEAKISLLKDKGNAALQAN 116
LF D F+ L +D TK S VQ+ K + KDP + + +I + K +
Sbjct: 69 LFPDDPEFI-LLVDADTKFD--PDSIVQLYKAMDKDPEIGGVCGEIHPMGKKQGPLVMYQ 125
Query: 117 NFKEAI 122
F+ AI
Sbjct: 126 VFEYAI 131
>gnl|CDD|227124 COG4785, NlpI, Lipoprotein NlpI, contains TPR repeats [General
function prediction only].
Length = 297
Score = 27.1 bits (60), Expect = 4.0
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 113 LQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAF 146
QA NF A EA+ ++LD T + NR A
Sbjct: 110 TQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIAL 143
>gnl|CDD|219573 pfam07781, Reovirus_Mu2, Reovirus minor core protein Mu-2. This
family represents the Reovirus core protein Mu-2. Mu-2
is a microtubule associated protein and is thought to
play a key role in the formation and structural
organisation of reovirus inclusion bodies.
Length = 735
Score = 27.1 bits (60), Expect = 4.3
Identities = 13/43 (30%), Positives = 18/43 (41%)
Query: 55 ANLFSDPNIFVQLQLDPRTKPFLSDPSYVQMIKEIQKDPSLMT 97
A SDP ++ +DP KP S PS + + P T
Sbjct: 240 ARYLSDPLALLRRLVDPSLKPLWSTPSDARAARLSGLRPQAAT 282
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 26.3 bits (59), Expect = 5.4
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 106 KDKGNAALQANNFKEAIEAYSEAIK 130
+K L+ N EA E + A+
Sbjct: 100 LEKALELLREGNRSEARECFQRAVD 124
>gnl|CDD|182415 PRK10370, PRK10370, formate-dependent nitrite reductase complex
subunit NrfG; Provisional.
Length = 198
Score = 26.4 bits (58), Expect = 5.8
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 77 LSDPSYVQMIKEIQKDPSLMTLEAKISLLKDKGNAALQA---------NNFKEAIEAYSE 127
L+DP + Q + + L L+ KI + N+ A N++ A+ AY +
Sbjct: 42 LADPLH-QFASQQTPEAQLQALQDKIR--ANPQNSEQWALLGEYYLWRNDYDNALLAYRQ 98
Query: 128 AIKLDGTNHILFS 140
A++L G N L++
Sbjct: 99 ALQLRGENAELYA 111
>gnl|CDD|181775 PRK09314, PRK09314, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 339
Score = 26.5 bits (59), Expect = 5.9
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 8/39 (20%)
Query: 31 EQMKEAIKDVRNQEMNDM-------NRGD-PFANLFSDP 61
++++EAI+D++N +M M N GD +A +FS P
Sbjct: 4 KRVEEAIEDIKNGKMLIMVDDEDRENEGDLVYAAIFSTP 42
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists 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. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 26.5 bits (59), Expect = 6.2
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 59 SDPNIFVQLQLDPRTKPFLSDPSYVQMIKEIQKDPS 94
SDPN +L LD R P LS + V +++++ K +
Sbjct: 224 SDPNDPTKLGLDLR--PVLSLKAKVILVRKVAKGEA 257
>gnl|CDD|201110 pfam00245, Alk_phosphatase, Alkaline phosphatase.
Length = 421
Score = 26.6 bits (59), Expect = 6.6
Identities = 30/139 (21%), Positives = 54/139 (38%), Gaps = 14/139 (10%)
Query: 8 SYLGRYKESISTYEEGLKLDPNN---EQMKEAIKDVRN-QEMN---DMNRGDPFANLFSD 60
Y + G +LD N E + V + E+ D P LF+D
Sbjct: 163 KYFFPTGTPDPYGQRGTRLDGRNLIQEWKHAGYQYVWDRTELLKAKDSPSVTPLLGLFAD 222
Query: 61 PNIFVQLQLDPRTKPFLSDPSYVQMIKEIQKDPS---LMTLEAKISLLKDKGNAALQ--- 114
++ ++ DP T P L + + V I+ + ++P LM +I + +A
Sbjct: 223 GDMPYEIPRDPATDPSLKEMTEVA-IRLLSRNPKGFFLMVEGGRIDHAHHENDACGALGE 281
Query: 115 ANNFKEAIEAYSEAIKLDG 133
+F +A++A E K +
Sbjct: 282 TVDFDQAVKAALEFAKSEK 300
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 25.0 bits (55), Expect = 6.8
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 101 KISLLKDKGNAALQANNFKEAIEAYSEAIKLD 132
L + L ++ EA+E +A+ L
Sbjct: 45 TARALNNLARLYLALGDYDEALEYLEKALALR 76
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 26.6 bits (59), Expect = 6.9
Identities = 8/30 (26%), Positives = 17/30 (56%)
Query: 109 GNAALQANNFKEAIEAYSEAIKLDGTNHIL 138
G+ L+ ++ AI+AY +A+K ++
Sbjct: 710 GDLYLRQKDYPAAIQAYRKALKRAPSSQNA 739
>gnl|CDD|197213 cd09114, PLDc_PPK1_C1, Catalytic C-terminal domain, first repeat,
of prokaryotic polyphosphate kinase 1 and similar
proteins. Catalytic C-terminal domain, first repeat (C1
domain), of bacterial polyphosphate kinases 1 (Poly P
kinase 1 or PPK1, EC 2.7.4.1) and similar proteins.
Inorganic polyphosphate (Poly P) plays an important role
in bacterial stress responses and stationary-phase
survival. PPK1 is the key enzyme responsible for the
synthesis of Poly P in bacteria. It can catalyze the
reversible conversion of the terminal-phosphate of ATP
to Poly P. Therefore, PPK1 is essential for bacterial
motility, quorum sensing, biofilm formation, and the
production of virulence factors and may serve as an
attractive antimicrobial drug target. Dimerization is
crucial for the enzymatic activity of PPK1. Each PPK1
monomer includes four structural domains, the N-terminal
(N) domain, the head (H) domain, and two closely related
C-terminal (C1 and C2) domains. The N domain provides
the upper binding interface for the adenine ring of the
ATP. The H domain is involved in dimerization, while
both the C1 and C2 domains contain residues crucial for
catalytic activity. The intersection of the N, C1, and
C2 domains forms a structural tunnel in which the PPK
catalytic reactions are carried out. In spite of the
lack of sequence homology, the C1 and C2 domains of PPK1
are structurally similar to the two repetitive catalytic
domains of phospholipase D (PLD). Moreover, some
residues in the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) of the PLD
superfamily are spatially conserved in the active site
of PPK1. It is possible that the bacterial PPK1 family
and the PLD family have a common ancestor and diverged
early in evolution. There is a second bacterial-type
enzyme, PPK2, which is involved in the synthesis of poly
P from GTP or ATP. PPK2 shows no sequence similarity to
PPK1 and belongs to different superfamily.
Length = 162
Score = 26.0 bits (57), Expect = 7.4
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 75 PFLSDPSYVQMIKEIQKDPSLMTLEAKISLLKDKGNAAL------QANNFKEAIEAYSEA 128
P+ S +Q++++ DP ++ + KI++ + + + A N KE
Sbjct: 16 PYESFEPVLQLLRQASTDPEVLAI--KITIYRLAKKSRIVDYLCAAAENGKEVTVVIELR 73
Query: 129 IKLDGTNHILFSNR 142
+ D N+I ++ R
Sbjct: 74 ARFDEENNIDWAER 87
>gnl|CDD|236875 PRK11189, PRK11189, lipoprotein NlpI; Provisional.
Length = 296
Score = 26.0 bits (58), Expect = 8.2
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 113 LQANNFKEAIEAYSEAIKLDGTNHILFSNRSAAF 146
QA NF A EA+ ++LD T + + NR A
Sbjct: 109 TQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIAL 142
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
0.314 0.130 0.358
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,470,317
Number of extensions: 661028
Number of successful extensions: 754
Number of sequences better than 10.0: 1
Number of HSP's gapped: 750
Number of HSP's successfully gapped: 77
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.3 bits)