RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780401|ref|YP_003064814.1| tetraacyldisaccharide
4'-kinase [Candidatus Liberibacter asiaticus str. psy62]
(338 letters)
>gnl|CDD|145645 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family
consists of tetraacyldisaccharide-1-P 4'-kinase also
known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyses the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer (LPS).
The family contains a P-loop motif at the N terminus.
Length = 318
Score = 299 bits (768), Expect = 7e-82
Identities = 123/314 (39%), Positives = 176/314 (56%), Gaps = 25/314 (7%)
Query: 16 SFFLYPISWIYSFISS---KLMKRG--QRLHAPIPVICVGGFVMGGTGKTPTALAIAKAV 70
+ L P+S +Y I++ L +RG + P+PVI VG +GGTGKTP +A+A+ +
Sbjct: 2 ALLLLPLSLLYGLIAALRRALYRRGILKSYRLPVPVIVVGNITVGGTGKTPLVIALAELL 61
Query: 71 IDKNLKPGFLSRGYGRKSRISFRVDLEKHSAYDVGDEPLLLARR--AVTIVTSDRKIGVQ 128
+ L+PG LSRGYG KS+ VD SA +VGDEPLLLARR +V DR +
Sbjct: 62 RARGLRPGVLSRGYGGKSKGPVLVD-PGSSAAEVGDEPLLLARRTPVPVVVGPDRAAAAR 120
Query: 129 MLLQE-GVDIIIMDDGFHSADLQADFSLIVVNSHRGLGNGLVFPAGPLRVPLSRQLSYVD 187
LL+ G D+II+DDGF L D ++VV+ RG GNG + PAGPLR PLSR L D
Sbjct: 121 ALLEAHGADVIILDDGFQHYRLARDLEIVVVDGARGFGNGRLLPAGPLREPLSR-LKRAD 179
Query: 188 AILYVGNKKNVISSIKNKSVYFAKLKPRL--------TFDLSGKKVLAFSGIADTEKFFT 239
A++ + + I V A+L+P L+GK+VLAF+GI + ++FF
Sbjct: 180 AVI-LNGGEAADPEIAEAPVLRARLEPSAAVNLADGERRPLAGKRVLAFAGIGNPQRFFD 238
Query: 240 TVRQLGALIEQCYSFGDHAHLSDKKIAYLLDQAQQKGLILVTTAKDAMRLHKRPGRAEEI 299
T+R LG + +F DH + +A+L +A++ G LVTT KDA++L E +
Sbjct: 239 TLRALGLEVVATLAFPDHHPFTAADLAFLEAEAKEPG--LVTTEKDAVKLRGDNLFDERL 296
Query: 300 FAKSMVIEVDIVFE 313
+ V+ V+ E
Sbjct: 297 W----VLPVEAELE 306
>gnl|CDD|31849 COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope
biogenesis, outer membrane].
Length = 336
Score = 282 bits (724), Expect = 8e-77
Identities = 124/323 (38%), Positives = 180/323 (55%), Gaps = 17/323 (5%)
Query: 5 PLFWWKARGFYSFFLYPISWIYSFISSKLMKRGQRLH--APIPVICVGGFVMGGTGKTPT 62
FW+ + +F L P+SW+Y+FI+ K ++ AP+PVICVG +GGTGKTP
Sbjct: 6 ERFWYGPSPWLAFLLLPLSWLYAFIAGLRRKLAKKGSYRAPVPVICVGNLTVGGTGKTPV 65
Query: 63 ALAIAKAVIDKNLKPGFLSRGYGRKSRISFRVDLEKHSAYDVGDEPLLLARR--AVTIVT 120
+ +A+A+ + ++ G +SRGYG K ++ VD +A +VGDEPLLLARR A V+
Sbjct: 66 VIWLAEALQARGVRVGVVSRGYGGKLKVVPLVDNIHTTAAEVGDEPLLLARRTGAPVAVS 125
Query: 121 SDRKIGVQMLL--QEGVDIIIMDDGFHSADLQADFSLIVVNSHRGLGNGLVFPAGPLRVP 178
DRK + LL G DII++DDG L DF ++VV+ RG GNG + PAGPLR P
Sbjct: 126 PDRKDAAKALLAAHLGCDIIVLDDGLQHYRLHRDFEIVVVDGQRGFGNGFLLPAGPLREP 185
Query: 179 LSRQLSYVDAILYVG-----NKKNVISSIKNKSVYFAKLKPRLTFDLSGKKVLAFSGIAD 233
R L DAI+ G + + + + A + DL GK+V+AF+GI +
Sbjct: 186 PKR-LKSADAIITNGGGSRADPIPMRLAPGHAPNLVAPGERSDVADLKGKRVVAFAGIGN 244
Query: 234 TEKFFTTVRQLGALIEQCYSFGDHAHLSDKKIAYLLDQAQQKGLILVTTAKDAMRLHKRP 293
++FF T+R LG + + +F DH S + L +AQ GL+ TT KDA++L
Sbjct: 245 PQRFFATLRNLGIQVVETLAFPDHYDFSAADLEDLAKKAQADGLL--TTEKDAVKL---R 299
Query: 294 GRAEEIFAKSMVIEVDIVFENPD 316
A E V+ +++ FE PD
Sbjct: 300 DFAPENVWNLPVLAIELSFELPD 322
>gnl|CDD|36207 KOG0989, KOG0989, KOG0989, Replication factor C, subunit RFC4
[Replication, recombination and repair].
Length = 346
Score = 29.1 bits (65), Expect = 1.7
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 56 GTGKTPTALAIAKAVIDKNLKP 77
GTGKT TALA A+A+ + L P
Sbjct: 67 GTGKTSTALAFARALNCEQLFP 88
>gnl|CDD|112618 pfam03814, KdpA, Potassium-transporting ATPase A subunit.
Length = 555
Score = 28.8 bits (65), Expect = 2.4
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 312 FENPDDLTNLVEM 324
FENP LTNLVE+
Sbjct: 242 FENPTPLTNLVEI 254
>gnl|CDD|173796 cd04857, Peptidases_S8_Tripeptidyl_Aminopeptidase_II, Peptidase S8
family domain in Tripeptidyl aminopeptidases_II.
Tripeptidyl aminopeptidases II are member of the
peptidase S8 or Subtilase family. Subtilases, or
subtilisin-like serine proteases, have an Asp/His/Ser
catalytic triad similar to that found in trypsin-like
proteases, but do not share their three-dimensional
structure (an example of convergent evolution).
Tripeptidyl aminopeptidase II removes tripeptides from
the free N terminus of oligopeptides as well as having
endoproteolytic activity. Some tripeptidyl
aminopeptidases have been shown to cleave tripeptides
and small peptides, e.g. angiotensin II and glucagon,
while others are believed to be involved in MHC I
processing.
Length = 412
Score = 28.0 bits (63), Expect = 3.5
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 241 VRQLGALIEQC-----YSFGDHAHLSDK-KIAYLLDQAQQK-GLILVTTA 283
VR + A IE S+G+ H + +I L+++A K G+I V++A
Sbjct: 234 VRAMIAAIETKCDLINMSYGEATHWPNSGRIIELMNEAVNKHGVIFVSSA 283
>gnl|CDD|32243 COG2060, KdpA, K+-transporting ATPase, A chain [Inorganic ion
transport and metabolism].
Length = 560
Score = 27.8 bits (62), Expect = 3.9
Identities = 11/13 (84%), Positives = 11/13 (84%)
Query: 312 FENPDDLTNLVEM 324
FENP LTNLVEM
Sbjct: 247 FENPTALTNLVEM 259
>gnl|CDD|33059 COG3248, Tsx, Nucleoside-binding outer membrane protein [Cell
envelope biogenesis, outer membrane].
Length = 284
Score = 28.1 bits (62), Expect = 4.0
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 185 YVDAILYVGNKKNVISSIKNKSVYFAKLKPRLTFD 219
Y DA + GN I N F +++PR + D
Sbjct: 79 YADAPNFGGNSDA--KGIWNHP-LFMEIEPRFSID 110
>gnl|CDD|33495 COG3700, AphA, Acid phosphatase (class B) [General function
prediction only].
Length = 237
Score = 27.7 bits (61), Expect = 4.3
Identities = 26/118 (22%), Positives = 46/118 (38%), Gaps = 4/118 (3%)
Query: 220 LSGKKVLAFS-GIADTEKFFTTVRQLGALIEQCYSFGDHAHLSDKKIAYLLDQAQQKGLI 278
L G+ +A S I DT F + G ++ +S G +L ++ ++ + I
Sbjct: 58 LEGRPPIAVSFDIDDTVLFSSPGFWRG---KKYFSPGSEDYLKNQVFWEKVNNGWDEFSI 114
Query: 279 LVTTAKDAMRLHKRPGRAEEIFAKSMVIEVDIVFENPDDLTNLVEMTVVSFANSNKKP 336
A+ + +H+R G A + D V + ++ M V FA KP
Sbjct: 115 PKEVARQLIDMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHITNMNPVIFAGDKPKP 172
>gnl|CDD|132938 cd06607, STKc_TAO, Catalytic domain of the Protein Serine/Threonine
Kinase, Thousand-and-one amino acids proteins.
Serine/threonine kinases (STKs), thousand-and-one amino
acids (TAO) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The TAO subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. TAO proteins possess mitogen-activated protein
kinase (MAPK) kinase kinase (MAPKKK or MAP3K or MKKK)
activity. They activate the MAPKs, p38 and c-Jun
N-terminal kinase (JNK), by phosphorylating and
activating the respective MAP/ERK kinases (MEKs, also
known as MKKs or MAPKKs), MEK3/MEK6 and MKK4/MKK7. MAPK
signaling cascades are important in mediating cellular
responses to extracellular signals. Vertebrates contain
three TAO subfamily members, named TAO1, TAO2, and TAO3.
Length = 307
Score = 27.8 bits (62), Expect = 4.4
Identities = 24/99 (24%), Positives = 49/99 (49%), Gaps = 12/99 (12%)
Query: 206 SVYFAKLKPRLTFDLSGKKVLAFSGIADTEKFFTTVRQLGALIEQCYSFGDHAHLSDKKI 265
+VYFA+ T ++ K +++SG EK+ ++++ ++Q H + + K
Sbjct: 30 AVYFARDV--RTNEVVAIKKMSYSGKQSNEKWQDIIKEV-RFLQQL----RHPNTIEYKG 82
Query: 266 AYLLDQAQQKGLIL---VTTAKDAMRLHKRPGRAEEIFA 301
YL + L++ + +A D + +HK+P + EI A
Sbjct: 83 CYLREHTAW--LVMEYCLGSASDILEVHKKPLQEVEIAA 119
>gnl|CDD|33174 COG3367, COG3367, Uncharacterized conserved protein [Function
unknown].
Length = 339
Score = 27.2 bits (60), Expect = 6.2
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 43 PIPVICVGGFVMGGTGKTPTALAIAKAVIDKNLKPGFLSRG 83
V+ V G GK TAL + +A ++ +K GF++ G
Sbjct: 147 DAKVVLVVGTDCA-VGKRTTALELREAAREEGIKAGFVATG 186
>gnl|CDD|176205 cd08243, quinone_oxidoreductase_like_1, Quinone oxidoreductase
(QOR). NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 320
Score = 27.2 bits (61), Expect = 6.6
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 110 LLARRAVTIVTSDRKIGVQMLLQE-GVDIIIMDDGFHSADLQAD 152
L T+ + R LL+E G D +++DDG + L+A
Sbjct: 162 LAKALGATVTATTRSPERAALLKELGADEVVIDDGAIAEQLRAA 205
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast
Rrp6p, human polymyositis/scleroderma autoantigen
100kDa, and similar proteins. Yeast Rrp6p and its human
homolog, the polymyositis/scleroderma autoantigen 100kDa
(PM/Scl-100), are exosome-associated proteins involved
in the degradation and processing of precursors to
stable RNAs. Both proteins contain a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. The motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. PM/Scl-100, an
autoantigen present in the nucleolar compartment of the
cell, reacts with autoantibodies produced by about 50%
of patients with polymyositis-scleroderma overlap
syndrome.
Length = 192
Score = 26.8 bits (60), Expect = 8.7
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 5/21 (23%)
Query: 144 FHSAD-----LQADFSLIVVN 159
FH AD LQ DF L VVN
Sbjct: 82 FHGADSDIIWLQRDFGLYVVN 102
>gnl|CDD|30329 cd02844, PAZ_CAF_like, PAZ domain, CAF_like subfamily. CAF (for
carpel factory) is a plant homolog of Dicer. CAF has
been implicated in flower morphogenesis and in early
Arabidopsis development and might function through
posttranscriptional regulation of specific mRNA
molecules. PAZ domains are named after the proteins
Piwi, Argonaut, and Zwille. PAZ is found in two families
of proteins that are essential components of
RNA-mediated gene-silencing pathways, including RNA
interference, the Piwi and Dicer families. PAZ functions
as a nucleic-acid binding domain, with a strong
preference for single-stranded nucleic acids (RNA or
DNA) or RNA duplexes with single-stranded 3' overhangs.
It has been suggested that the PAZ domain provides a
unique mode for the recognition of the two 3'-terminal
nucleotides in single-stranded nucleic acids and buries
the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes..
Length = 135
Score = 26.8 bits (59), Expect = 9.1
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 168 LVFPAGPLRVPLSRQLSYVDAILYVGNKKNVISSIKNKSVYFAKLKPRL 216
L P PL +Q+ + +L+ ++ S K K YF +L P L
Sbjct: 82 LNHPNQPLLK--GKQIFNLHNLLHNRFEEKGESEEKEKDRYFVELPPEL 128
>gnl|CDD|143458 cd07140, ALDH_F1L_FTFDH, 10-formyltetrahydrofolate dehydrogenase,
ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase
(FTHFDH, EC=1.5.1.6), also known as aldehyde
dehydrogenase family 1 member L1 (ALDH1L1) in humans, is
a multi-domain homotetramer with an N-terminal formyl
transferase domain and a C-terminal ALDH domain. FTHFDH
catalyzes an NADP+-dependent dehydrogenase reaction
resulting in the conversion of 10-formyltetrahydrofolate
to tetrahydrofolate and CO2. The ALDH domain is also
capable of the oxidation of short chain aldehydes to
their corresponding acids.
Length = 486
Score = 26.7 bits (59), Expect = 9.8
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 54 MGGTGKTPTALAIAKAVIDKNLKPGFLSRGYGRKSRISFR-VDLEK 98
+G TG TP I K+ NLK L G G+ I F D++K
Sbjct: 230 LGFTGSTPIGKHIMKSCAVSNLKKVSLELG-GKSPLIIFADCDMDK 274
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.323 0.139 0.409
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,072,753
Number of extensions: 219542
Number of successful extensions: 645
Number of sequences better than 10.0: 1
Number of HSP's gapped: 635
Number of HSP's successfully gapped: 29
Length of query: 338
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 244
Effective length of database: 4,232,491
Effective search space: 1032727804
Effective search space used: 1032727804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)