RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781223|ref|YP_003065636.1| intrrupted gp229, phage
associated protein [Candidatus Liberibacter asiaticus str. psy62]
(110 letters)
>gnl|CDD|31246 COG1044, LpxD, UDP-3-O-[3-hydroxymyristoyl].
Length = 338
Score = 41.4 bits (97), Expect = 6e-05
Identities = 17/93 (18%), Positives = 31/93 (33%)
Query: 8 RDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIV 67
A + A + A + N + N + +G + A +G N +
Sbjct: 91 LFYRPFNPAAGIHPTAVIDPTATIGKNVSIGPNVVIGAGVVIGENVVIGAGAVIGENVKI 150
Query: 68 RDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100
D + + + VI N + AV+G D
Sbjct: 151 GDGTVIHPNVTIYHNVVIGNNVIIHSGAVIGAD 183
Score = 29.1 bits (65), Expect = 0.26
Identities = 12/69 (17%), Positives = 28/69 (40%)
Query: 41 TYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100
+ A + A + N S+G N ++ +G + + VI N ++ V+ +
Sbjct: 100 AGIHPTAVIDPTATIGKNVSIGPNVVIGAGVVIGENVVIGAGAVIGENVKIGDGTVIHPN 159
Query: 101 TVVEGDTVL 109
+ + V+
Sbjct: 160 VTIYHNVVI 168
Score = 26.8 bits (59), Expect = 1.3
Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 1/90 (1%)
Query: 10 CATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRD 69
T ID + + + ++ + ++ N + ++ + G ++G+ +G I+
Sbjct: 213 ANTTIDRGAL-DDTVIGEGVKIDNLVQIGHNVRIGEHCIIAGQVGIAGSVKIGKYVIIGG 271
Query: 70 TAEVGGDAFVIGFTVISGNARVRGNAVVGG 99
+ G + I + V + G
Sbjct: 272 QVGIAGHLEIGDGVTIGARSGVMASITEPG 301
>gnl|CDD|32354 COG2171, DapD, Tetrahydrodipicolinate N-succinyltransferase [Amino
acid transport and metabolism].
Length = 271
Score = 36.4 bits (84), Expect = 0.002
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 8/107 (7%)
Query: 12 TVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTA 71
V + R+ A V A + V ++V A G V G ASVG A V +
Sbjct: 104 FVPEGVRIVPGAIVRLGAYIAKGTVVMPESFVNIGAGTGEGTMVDGRASVGSCAQVGKNS 163
Query: 72 EVGGDAFVIGF--------TVISGNARVRGNAVVGGDTVVEGDTVLE 110
+GG A + G +I N + N+ V +V V+
Sbjct: 164 HIGGGASIGGVLEPLQANPVIIGDNCLIGANSEVVEGVIVGDGCVVA 210
Score = 28.7 bits (64), Expect = 0.38
Identities = 28/113 (24%), Positives = 38/113 (33%), Gaps = 14/113 (12%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVG 62
A+VR A + V + V A + T V A VG A+V N+ +G
Sbjct: 113 PGAIVRLGAYIAK------GTVVMPESFVNIGAGTGEGTMVDGRASVGSCAQVGKNSHIG 166
Query: 63 GNAIVRDTAEVG-------GDAFVIGFTVISGNA-RVRGNAVVGGDTVVEGDT 107
G A + E GD +IG V VV + DT
Sbjct: 167 GGASIGGVLEPLQANPVIIGDNCLIGANSEVVEGVIVGDGCVVAAGVFITQDT 219
>gnl|CDD|34410 COG4801, COG4801, Predicted acyltransferase [General function
prediction only].
Length = 277
Score = 35.3 bits (81), Expect = 0.004
Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 5/110 (4%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVR-----DNAKVGGYAKVSG 57
N V + V+ + G S+ ++ V V + + + ++ + KV+G
Sbjct: 8 PNTRVEEAIIVVKGDVIIGKNSMLKYGVVGEEIIVGERVRIYGDIVAKDIRIDMWCKVTG 67
Query: 58 NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDT 107
N V +A + + + + G VIG I + + G V G V+
Sbjct: 68 NVIVENDAYIGEFSSIKGKLTVIGDLDIGADVIIEGGFVAKGWIVIRNPV 117
>gnl|CDD|100038 cd00208, LbetaH, Left-handed parallel beta-Helix (LbetaH or LbH)
domain: The alignment contains 5 turns, each containing
three imperfect tandem repeats of a hexapeptide repeat
motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity, however, some subfamilies in
this hierarchy also show activities related to ion
transport or translation initiation. Many are trimeric
in their active forms..
Length = 78
Score = 34.5 bits (80), Expect = 0.006
Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 2/77 (2%)
Query: 29 AQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAE--VGGDAFVIGFTVIS 86
+ ++ +R +G + A +G + +G + + VI
Sbjct: 1 VFIGEGVKIHPKAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNPTIIGDNVEIGANAVIH 60
Query: 87 GNARVRGNAVVGGDTVV 103
G ++ NAV+G VV
Sbjct: 61 GGVKIGDNAVIGAGAVV 77
Score = 31.5 bits (72), Expect = 0.060
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 47 AKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGF--------TVISGNARVRGNAVVG 98
+G K+ A + G ++ D +G A + T+I N + NAV+
Sbjct: 1 VFIGEGVKIHPKAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNPTIIGDNVEIGANAVIH 60
Query: 99 GDTVVEGDTVL 109
G + + V+
Sbjct: 61 GGVKIGDNAVI 71
Score = 30.3 bits (69), Expect = 0.13
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGG 63
AV+R + D+ + A + T + DN ++G A + G +G
Sbjct: 12 KAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNP----TIIGDNVEIGANAVIHGGVKIGD 67
Query: 64 NAIV 67
NA++
Sbjct: 68 NAVI 71
>gnl|CDD|100039 cd00710, LbH_gamma_CA, Gamma carbonic anhydrases (CA): Carbonic
anhydrases are zinc-containing enzymes that catalyze the
reversible hydration of carbon dioxide in a two-step
mechanism, involving the nucleophilic attack of a
zinc-bound hydroxide ion on carbon dioxide, followed by
the regeneration of the active site by ionization of the
zinc-bound water molecule and removal of a proton from
the active site. They are ubiquitous enzymes involved in
fundamental processes like photosynthesis, respiration,
pH homeostasis and ion transport. There are three
distinct groups of carbonic anhydrases - alpha, beta
and gamma - which show no significant sequence identity
or structural similarity. Gamma CAs are homotrimeric
enzymes, with each subunit containing a left-handed
parallel beta helix (LbH) structural domain..
Length = 167
Score = 33.4 bits (77), Expect = 0.015
Identities = 33/113 (29%), Positives = 52/113 (46%), Gaps = 9/113 (7%)
Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNA----EVSDNTYVRDN----AKVGGYAKV 55
+A V A VI D + N V A ++++ + N ++D A G +
Sbjct: 8 SAYVHPTAVVIGDVIIGDNVFVGPGASIRADEGTPIIIGANVNIQDGVVIHALEGYSVWI 67
Query: 56 SGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTV 108
N S+ AIV A +G + F IGF + NA+V N V+G + VV+G +
Sbjct: 68 GKNVSIAHGAIVHGPAYIGDNCF-IGFRSVVFNAKVGDNCVIGHNAVVDGVEI 119
>gnl|CDD|31007 COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine
patch superfamily [General function prediction only].
Length = 176
Score = 33.2 bits (76), Expect = 0.016
Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 8/115 (6%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAE---VSDNTYVRDNAKVGGYAK----V 55
A V ATVI D R+ S+ A ++ + E + T ++D + +
Sbjct: 16 PTAFVAPSATVIGDVRIGAGVSIWPGAVLRGDVEPIRIGARTNIQDGVVIHADPGYPVTI 75
Query: 56 SGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110
+ ++G A+V +G + + + A + ++VG +V +
Sbjct: 76 GDDVTIGHGAVVH-GCTIGDNVLIGMGATVLDGAVIGDGSIVGAGALVTPGKEIP 129
>gnl|CDD|100060 cd05636, LbH_G1P_TT_C_like, Putative glucose-1-phosphate
thymidylyltransferase, C-terminal Left-handed parallel
beta-Helix (LbH) domain: Proteins in this family show
simlarity to glucose-1-phosphate adenylyltransferases in
that they contain N-terminal catalytic domains that
resemble a dinucleotide-binding Rossmann fold and
C-terminal LbH fold domains. Members in this family are
predicted to be glucose-1-phosphate
thymidylyltransferases, which are involved in the
dTDP-L-rhamnose biosynthetic pathway.
Glucose-1-phosphate thymidylyltransferase catalyzes the
synthesis of deoxy-thymidine di-phosphate
(dTDP)-L-rhamnose, an important component of the cell
wall of many microorganisms. The C-terminal LbH domain
contains multiple turns, each containing three imperfect
tandem repeats of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity..
Length = 163
Score = 32.6 bits (75), Expect = 0.025
Identities = 18/58 (31%), Positives = 24/58 (41%)
Query: 46 NAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVV 103
V + G +G AIVR A + G + I NA +RG V+G VV
Sbjct: 5 EGTVEEGVTIKGPVWIGEGAIVRSGAYIEGPVIIGKGCEIGPNAYIRGYTVLGDGCVV 62
Score = 28.7 bits (65), Expect = 0.40
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92
V + ++ +G A V A + G I+ E+G +A++ G+TV+ V
Sbjct: 4 IEGTVEEGVTIKGPVWIGEGAIVRSGAYIEGPVIIGKGCEIGPNAYIRGYTVLGDGCVV- 62
Query: 93 GNAV 96
GN+V
Sbjct: 63 GNSV 66
>gnl|CDD|36673 KOG1460, KOG1460, KOG1460, GDP-mannose pyrophosphorylase
[Carbohydrate transport and metabolism, Cell
wall/membrane/envelope biogenesis, Posttranslational
modification, protein turnover, chaperones].
Length = 407
Score = 31.8 bits (72), Expect = 0.041
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92
+ AE+ + Y+ +AKV AK+ N S+G N V G + ++I +A +
Sbjct: 281 TQAEIIGDVYIHPSAKVHPTAKIGPNVSIGANVRV-------GPGVRLRESIILDDAEIE 333
Query: 93 GNAVV 97
NAVV
Sbjct: 334 ENAVV 338
>gnl|CDD|31400 COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase
(contains nucleotidyltransferase and I-patch
acetyltransferase domains) [Cell envelope biogenesis,
outer membrane].
Length = 460
Score = 31.7 bits (72), Expect = 0.046
Identities = 23/127 (18%), Positives = 52/127 (40%), Gaps = 24/127 (18%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRD-----NAKVGGYAKVS- 56
DNAV++ +VI+ + V A+V FA+++ A + + ++ + A +G +K
Sbjct: 308 DNAVIKA-YSVIEGSTVGEGATVGPFARLRPGAVLGADVHIGNFVEVKKATIGKGSKAGH 366
Query: 57 ----GNASVGGNAIV-------------RDTAEVGGDAFVIGFTVISGNARVRGNAVVGG 99
G+A +G N + + +G + F+ + + + A +
Sbjct: 367 LTYLGDAEIGENVNIGAGTITCNYDGKNKFKTIIGDNVFIGSNSQLVAPVTIGDGATIAA 426
Query: 100 DTVVEGD 106
+ + D
Sbjct: 427 GSTITKD 433
Score = 24.4 bits (53), Expect = 6.4
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 67 VRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110
+R E+G D VI N + GN V+G + V+ +V++
Sbjct: 265 IRGDVEIGRD------VVIEPNVILEGNTVIGDNVVIGPGSVIK 302
Score = 24.0 bits (52), Expect = 9.8
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 39 DNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVG 98
TY+R + ++G + N + GN ++ GD VIG + ++ + NAV+
Sbjct: 261 ATTYIRGDVEIGRDVVIEPNVILEGNTVI-------GDNVVIGPGSVIKDSVIGDNAVIK 313
Query: 99 GDTVVEGDTV 108
+V+EG TV
Sbjct: 314 AYSVIEGSTV 323
>gnl|CDD|31245 COG1043, LpxA, Acyl-[acyl carrier protein].
Length = 260
Score = 31.3 bits (71), Expect = 0.053
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 65 AIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVL 109
AI+ AE+G D + F +I N + V+ VVEG T +
Sbjct: 10 AIIEPGAEIGEDVKIGPFCIIGPNVEIGDGTVLKSHVVVEGHTTI 54
Score = 29.0 bits (65), Expect = 0.27
Identities = 15/58 (25%), Positives = 24/58 (41%)
Query: 43 VRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100
+ A++G K+ +G N + D + V G T I N R+ A +G D
Sbjct: 12 IEPGAEIGEDVKIGPFCIIGPNVEIGDGTVLKSHVVVEGHTTIGRNNRIFPFASIGED 69
Score = 29.0 bits (65), Expect = 0.28
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 40 NTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGG 99
+V + +G ++ NA++ G+ V D A +GG + V F I +A + G + V
Sbjct: 118 YAHVAHDCVIGNNCILANNATLAGHVEVGDYAIIGGLSAVHQFVRIGAHAMIGGLSAVSQ 177
Query: 100 D 100
D
Sbjct: 178 D 178
>gnl|CDD|31247 COG1045, CysE, Serine acetyltransferase [Amino acid transport and
metabolism].
Length = 194
Score = 29.5 bits (66), Expect = 0.20
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 31 VKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNAR 90
+ A + D+ + +GG K SG + + +G A ++G I NA+
Sbjct: 90 IGETAVIGDDVTIYHGVTLGGTGKESGKRHP----TIGNGVYIGAGAKILGNIEIGDNAK 145
Query: 91 VRGNAVV 97
+ +VV
Sbjct: 146 IGAGSVV 152
Score = 24.5 bits (53), Expect = 7.8
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 32 KSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG 81
K + + + Y+ AK+ G ++ NA +G ++V +V +A V+G
Sbjct: 117 KRHPTIGNGVYIGAGAKILGNIEIGDNAKIGAGSVV--LKDVPPNATVVG 164
>gnl|CDD|100041 cd03350, LbH_THP_succinylT,
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP)
N-succinyltransferase (also called THP
succinyltransferase): THDP N-succinyltransferase
catalyzes the conversion of tetrahydrodipicolinate and
succinyl-CoA to N-succinyltetrahydrodipicolinate and
CoA. It is the committed step in the succinylase pathway
by which bacteria synthesize L-lysine and
meso-diaminopimelate, a component of peptidoglycan. The
enzyme is homotrimeric and each subunit contains an
N-terminal region with alpha helices and hairpin loops,
as well as a C-terminal region with a left-handed
parallel alpha-helix (LbH) structural motif encoded by
hexapeptide repeat motifs..
Length = 139
Score = 29.3 bits (66), Expect = 0.24
Identities = 25/112 (22%), Positives = 39/112 (34%), Gaps = 8/112 (7%)
Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKV------SG 57
V A + D A + A + + V A V + T V A VG A++ S
Sbjct: 1 GRRVPPGAIIRDGAFIGPGAVLMMPSYVNIGAYVDEGTMVDSWATVGSCAQIGKNVHLSA 60
Query: 58 NASVGG--NAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDT 107
A +GG + + D F+ + V AV+ V+ T
Sbjct: 61 GAVIGGVLEPLQATPVIIEDDVFIGANCEVVEGVIVGKGAVLAAGVVLTQST 112
>gnl|CDD|31401 COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase
involved in lipopolysaccharide biosynthesis/translation
initiation factor 2B, gamma/epsilon subunits
(eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis,
outer membrane / Translation, ribosomal structure and
biogenesis].
Length = 358
Score = 29.2 bits (65), Expect = 0.26
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 75 GDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110
A++IG VI A++ A++G TV+ +
Sbjct: 254 RSAYIIGPVVIGPGAKIGPGALIGPYTVIGEGVTIG 289
>gnl|CDD|100058 cd04745, LbH_paaY_like, paaY-like: This group is composed by
uncharacterized proteins with similarity to the protein
product of the E. coli paaY gene, which is part of the
paa gene cluster responsible for phenylacetic acid
degradation. Proteins in this group are expected to
adopt the left-handed parallel beta-helix (LbH)
structure. They contain imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Similarity to gamma carbonic anhydrase and
Ferripyochelin Binding Protein (FBP) may suggest metal
binding capacity..
Length = 155
Score = 29.3 bits (66), Expect = 0.27
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 41 TYVRDNAKVGGYAKVSG-----NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNA 95
T + +N +G A + G NA VG NA+V D A +G ++ V + + +
Sbjct: 62 TVLEENGHIGHGAILHGCTIGRNALVGMNAVVMDGAVIGEESIVGAMAFVKAGTVIPPRS 121
Query: 96 VVGG 99
++ G
Sbjct: 122 LIAG 125
>gnl|CDD|100044 cd03353, LbH_GlmU_C, N-acetyl-glucosamine-1-phosphate
uridyltransferase (GlmU), C-terminal left-handed
beta-helix (LbH) acetyltransferase domain: GlmU is also
known as UDP-N-acetylglucosamine pyrophosphorylase. It
is a bifunctional bacterial enzyme that catalyzes two
consecutive steps in the formation of
UDP-N-acetylglucosamine (UDP-GlcNAc), an important
precursor in bacterial cell wall formation. The two
enzymatic activities, uridyltransferase and
acetyltransferase, are carried out by two independent
domains. The C-terminal LbH domain possesses the
acetyltransferase activity. It catalyzes the
CoA-dependent acetylation of GlcN-1-phosphate to
GlcNAc-1-phosphate. The LbH domain contains 10 turns,
each containing three imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X. The
acetyltransferase active site is located at the
interface between two subunits of the active LbH
trimer..
Length = 193
Score = 28.9 bits (66), Expect = 0.30
Identities = 14/73 (19%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRD-----NAKVGGYAKVS- 56
D V++ ++VI+ A + A+V FA ++ + + ++ + + +G +K +
Sbjct: 55 DGVVIKA-SSVIEGAVIGNGATVGPFAHLRPGTVLGEGVHIGNFVEIKKSTIGEGSKANH 113
Query: 57 ----GNASVGGNA 65
G+A +G
Sbjct: 114 LSYLGDAEIGEGV 126
Score = 26.2 bits (59), Expect = 2.1
Identities = 8/42 (19%), Positives = 20/42 (47%)
Query: 67 VRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTV 108
+ E+G D + ++ G + + V+G + V++ T+
Sbjct: 12 IDGDVEIGVDVVIDPGVILEGKTVIGEDCVIGPNCVIKDSTI 53
>gnl|CDD|100043 cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase
(LpxD): The enzyme catalyzes the transfer of
3-hydroxymyristic acid or 3-hydroxy-arachidic acid,
depending on the organism, from the acyl carrier protein
(ACP) to UDP-3-O-acyl-glucosamine to produce
UDP-2,3-diacyl-GlcNAc. This constitutes the third step
in the lipid A biosynthetic pathway in Gram-negative
bacteria. LpxD is a homotrimer, with each subunit
consisting of a novel combination of an N-terminal
uridine-binding domain, a core lipid-binding left-handed
parallel beta helix (LbH) domain, and a C-terminal
alpha-helical extension. The LbH domain contains 9
turns, each containing three imperfect tandem repeats of
a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X)..
Length = 205
Score = 27.4 bits (62), Expect = 0.94
Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 28 FAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAF-----VIG- 81
A++ N + N + + +G +G ++ D +G D I
Sbjct: 1 SAKIGENVSIGPNAVIGEGVVIGD------GVVIGPGVVIGDGVVIGDDCVIHPNVTIYE 54
Query: 82 FTVISGNARVRGNAVVGGD 100
+I + AV+G D
Sbjct: 55 GCIIGDRVIIHSGAVIGSD 73
Score = 24.3 bits (54), Expect = 7.5
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 53 AKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVV 103
AK+ N S+G NA++ + +G VIG V+ G+ V+G D V+
Sbjct: 2 AKIGENVSIGPNAVIGEGVVIGDGV-VIGPGVVIGD-----GVVIGDDCVI 46
>gnl|CDD|100049 cd03359, LbH_Dynactin_5, Dynactin 5 (or subunit p25); Dynactin is a
major component of the activator complex that stimulates
dynein-mediated vesicle transport. Dynactin is a
heterocomplex of at least eight subunits, including a
150,000-MW protein called Glued, the actin-capping
protein Arp1, and dynamatin. In vitro binding
experiments show that dynactin enhances dynein-dependent
motility, possibly through interaction with microtubules
and vesicles. Subunit p25 is part of the pointed-end
subcomplex in dynactin that also includes p26, p27, and
Arp11. This subcomplex interacts with membranous
cargoes. p25 and p27 contain imperfect tandem repeats of
a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X),
indicating a left-handed parallel beta helix (LbH)
structural domain. Proteins containing hexapeptide
repeats are often enzymes showing acyltransferase
activity..
Length = 161
Score = 26.8 bits (60), Expect = 1.2
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASV 61
+N VV A + + N + R +K ++ D T V + + Y+ VSG +
Sbjct: 83 ENCVVN-AAQIGSYVHIGKNCVIGRRCIIKDCVKILDGTVVPPDTVIPPYSVVSGRPAR 140
Score = 26.0 bits (58), Expect = 2.6
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 15/68 (22%)
Query: 37 VSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG-FTVISGNARVRGNA 95
+ D ++ +N V A++ +G N VIG +I ++
Sbjct: 75 IGDYVFIGENCVVNA-AQIGSYVHIGKNC-------------VIGRRCIIKDCVKILDGT 120
Query: 96 VVGGDTVV 103
VV DTV+
Sbjct: 121 VVPPDTVI 128
>gnl|CDD|100059 cd05635, LbH_unknown, Uncharacterized proteins, Left-handed
parallel beta-Helix (LbH) domain: Members in this group
are uncharacterized bacterial proteins containing a LbH
domain with multiple turns, each containing three
imperfect tandem repeats of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity..
Length = 101
Score = 26.9 bits (60), Expect = 1.3
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 11 ATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGG 51
A + A + G + ++VK A + NT + K+GG
Sbjct: 18 AVIEPFAVIEGPVYIGPGSRVKMGARIYGNTTIGPTCKIGG 58
>gnl|CDD|34718 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 26.6 bits (58), Expect = 1.6
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 16 DARVSGNASVSRFAQVKSNAEVSDNTYVRDNA----KVGGYAKVSGNASVG 62
+ S A N S++++ R+N K +AK + AS+G
Sbjct: 311 ARKFSRFHYAVSLANSFMNLGTSNDSFYRNNLDWLGKASNWAKFTATASLG 361
>gnl|CDD|100042 cd03351, LbH_UDP-GlcNAc_AT, UDP-N-acetylglucosamine
O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins
in this family catalyze the transfer of
(R)-3-hydroxymyristic acid from its acyl carrier protein
thioester to UDP-GlcNAc. It is the first enzyme in the
lipid A biosynthetic pathway and is also referred to as
LpxA. Lipid A is essential for the growth of Escherichia
coli and related bacteria. It is also essential for
maintaining the integrity of the outer membrane.
UDP-GlcNAc acyltransferase is a homotrimer of
left-handed parallel beta helix (LbH) subunits. Each
subunit contains an N-terminal LbH region with 9 turns,
each containing three imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X),
and a C-terminal alpha-helical region..
Length = 254
Score = 26.2 bits (59), Expect = 1.8
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 65 AIVRDTAEVGGDAFVIG-FTVISGNARVRGNAVVGGDTVVEGDTVL 109
AIV A++G + IG F VI N + V+G V++G T +
Sbjct: 6 AIVDPGAKIGENV-EIGPFCVIGPNVEIGDGTVIGSHVVIDGPTTI 50
Score = 25.9 bits (58), Expect = 2.5
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 58 NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100
NA++ G+ + D A +GG + V F I +A V G + V D
Sbjct: 132 NATLAGHVEIGDYAIIGGLSAVHQFCRIGRHAMVGGGSGVVQD 174
Score = 25.5 bits (57), Expect = 3.6
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 37 VSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG----------FTVIS 86
+ +N + +NA + G+ ++ A +GG + V +G A V G + + +
Sbjct: 123 IGNNVILANNATLAGHVEIGDYAIIGGLSAVHQFCRIGRHAMVGGGSGVVQDVPPYVIAA 182
Query: 87 GN-ARVRGNAVVG 98
GN AR+RG +VG
Sbjct: 183 GNRARLRGLNLVG 195
Score = 24.7 bits (55), Expect = 5.6
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 53 AKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARV-RGN-----AVVGGD 100
AK+ N +G ++ E+G + VI G + + N A +G
Sbjct: 12 AKIGENVEIGPFCVIGPNVEIGDGTVIGSHVVIDGPTTIGKNNRIFPFASIGEA 65
>gnl|CDD|38331 KOG3121, KOG3121, KOG3121, Dynactin, subunit p25 [Cytoskeleton].
Length = 184
Score = 26.1 bits (57), Expect = 2.4
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 43 VRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGN-AVVGG 99
V + A++G Y + NA +G +++D + D + T++ + + GN A V G
Sbjct: 98 VVNAAQIGSYVHLGKNAVIGRRCVLKDCCRILDDTVLPPETLVPPYSTIGGNPAQVVG 155
>gnl|CDD|100051 cd04645, LbH_gamma_CA_like, Gamma carbonic anhydrase-like: This
family is composed of gamma carbonic anhydrase (CA),
Ferripyochelin Binding Protein (FBP), E. coli paaY
protein, and similar proteins. CAs are zinc-containing
enzymes that catalyze the reversible hydration of carbon
dioxide in a two-step mechanism, involving the
nucleophilic attack of a zinc-bound hydroxide ion on
carbon dioxide, followed by the regeneration of the
active site by ionization of the zinc-bound water
molecule and removal of a proton from the active site.
They are ubiquitous enzymes involved in fundamental
processes like photosynthesis, respiration, pH
homeostasis and ion transport. There are three
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Gamma CAs are
trimeric enzymes with left-handed parallel beta helix
(LbH) structural domain..
Length = 153
Score = 25.8 bits (58), Expect = 2.7
Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 58 NASVGGNAIVRDTAEVGGDAFV-IGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110
N +VG A++ +G + + +G ++ G A + ++V ++V V+
Sbjct: 66 NVTVGHGAVLHG-CTIGDNCLIGMGAIILDG-AVIGKGSIVAAGSLVPPGKVIP 117
>gnl|CDD|30459 COG0110, WbbJ, Acetyltransferase (isoleucine patch superfamily)
[General function prediction only].
Length = 190
Score = 25.2 bits (54), Expect = 4.2
Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 3/90 (3%)
Query: 11 ATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGN-ASVGGNAIVRD 69
V + + N V + +N+ D A VG G +G A++
Sbjct: 82 ILVGEGITIGDNVVVGPNVTIYTNSHPGDFVTANIGALVGAGPVTIGEDVWIGAGAVILP 141
Query: 70 TAEVGGDAFVIGFTVISGNARVRGNAVVGG 99
+G A + +V++ + V +V G
Sbjct: 142 GVTIGEGAVIGAGSVVTKD--VPPYGIVAG 169
>gnl|CDD|113132 pfam04349, MdoG, Periplasmic glucan biosynthesis protein, MdoG.
This family represents MdoG, a protein that is necessary
for the synthesis of periplasmic glucans. The function
of MdoG remains unknown. It has been suggested that it
may catalyse the addition of branches to a linear glucan
backbone.
Length = 484
Score = 24.4 bits (53), Expect = 6.3
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 23 ASVSRFAQVKSNAEVSDNTYVRDNAKVGGY 52
V+ + SNA V +N +R N + GY
Sbjct: 416 HPVTVEPSLHSNAGVVENVSLRYNPVIKGY 445
>gnl|CDD|100050 cd03360, LbH_AT_putative, Putative Acyltransferase (AT),
Left-handed parallel beta-Helix (LbH) domain; This group
is composed of mostly uncharacterized proteins
containing an N-terminal helical subdomain followed by a
LbH domain. The alignment contains 6 turns, each
containing three imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Proteins containing hexapeptide repeats are often
enzymes showing acyltransferase activity. A few members
are identified as NeuD, a sialic acid (Sia)
O-acetyltransferase that is required for Sia synthesis
and surface polysaccharide sialylation..
Length = 197
Score = 24.4 bits (54), Expect = 6.6
Identities = 14/76 (18%), Positives = 32/76 (42%)
Query: 22 NASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG 81
A ++ A++ N ++ + + +G + ++ + G + + A +G A +I
Sbjct: 108 GAVINPDARIGDNVIINTGAVIGHDCVIGDFVHIAPGVVLSGGVTIGEGAFIGAGATIIQ 167
Query: 82 FTVISGNARVRGNAVV 97
I A + AVV
Sbjct: 168 GVTIGAGAIIGAGAVV 183
>gnl|CDD|36924 KOG1712, KOG1712, KOG1712, Adenine phosphoribosyl transferases
[Nucleotide transport and metabolism].
Length = 183
Score = 24.4 bits (53), Expect = 6.8
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 57 GNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAV 96
G + + R AEV A VI + G +++G +
Sbjct: 136 GTLAAATELLERVGAEVVECACVIELPELKGREKLKGKPL 175
>gnl|CDD|100045 cd03354, LbH_SAT, Serine acetyltransferase (SAT): SAT catalyzes
the CoA-dependent acetylation of the side chain
hydroxyl group of L-serine to form O-acetylserine, as
the first step of a two-step biosynthetic pathway in
bacteria and plants leading to the formation of
L-cysteine. This reaction represents a key metabolic
point of regulation for the cysteine biosynthetic
pathway due to its feedback inhibition by cysteine. The
enzyme is a 175 kDa homohexamer, composed of a dimer of
homotrimers. Each subunit contains an N-terminal alpha
helical region and a C-terminal left-handed beta-helix
(LbH) subdomain with 5 turns, each containing a
hexapeptide repeat motif characteristic of the
acyltransferase superfamily of enzymes. The trimer
interface mainly involves the C-terminal LbH subdomain
while the dimer (of trimers) interface is mediated by
the N-terminal alpha helical subdomain..
Length = 101
Score = 24.3 bits (54), Expect = 8.5
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92
A + DN + +GG K G + + D +G A ++G I N ++
Sbjct: 27 ETAVIGDNCTIYQGVTLGGKGKGGG----KRHPTIGDNVVIGAGAKILGNITIGDNVKIG 82
Query: 93 GNAVV 97
NAVV
Sbjct: 83 ANAVV 87
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
0.313 0.131 0.358
Gapped
Lambda K H
0.267 0.0875 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,096,519
Number of extensions: 48460
Number of successful extensions: 225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 183
Number of HSP's successfully gapped: 84
Length of query: 110
Length of database: 6,263,737
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,621,453
Effective search space: 157129402
Effective search space used: 157129402
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 (21.9 bits)
S2: 51 (23.2 bits)