Current Annotation for L35480_AD106_G4 19/04/24

name
startcoord
endcoord
*
*
de
intron
start1
direction
status
gn
ec
gp
cc
type1
kognum
kog
glimmer
dompat
auth
10/10/03 00:00:00
More Comments
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
10/10/03 00:00:00
 
 
L35480_AD106_G4_056
4636
4439
 
 
Membrane-associated lipoprotein involved in thiamine biosynthesis (ApbE family)
 
1
R
ADDED
apbE
 
ApbE-like lipoprotein
 
PROTEIN
COG1477 Membrane-associated lipoprotein involved in thiamine biosynthesis
H Coenzyme transport and metabolism
-
 
82.227.62.180
10/09/07 21:09:32
 
 
LUAcid_AD106_G4_17
24163
24933
 
 
hypothetical protein
 
1
D
ADDED
 
 
hypothetical protein
one single match in Ellin345
PROTEIN
 
 
Good
 
82.227.62.180
10/09/07 21:42:06
 
 
luAcid_AD106_G4_16sRNA
17717
19275
 
 
rRNA
 
1
D
ADDED
16S
 
 
 
RNA
 
 
 
 
82.227.62.180
10/09/07 21:44:17
 
 
luAcid_AD106_G4_23sRNA
20415
23302
 
 
rRNA
 
1
D
ADDED
23S
 
 
 
RNA
 
 
 
 
82.227.62.180
10/09/07 21:44:38
 
 
LUAcid_AD106_G4_04
3281
1785
 
 
NhaC Na+/H+ antiporter
 
1
R
ADDED
nahC
 
NahC
best matches with Shewanella species
PROTEIN
COG1757 Na+/H+ antiporter
C Energy production and conversion
Good
 
82.227.62.180
10/09/07 22:34:09
 
 
LUAcid_AD106_G4_05
3372
4736
 
 
MiaB like protein tRNA modifiying enzyme
 
1
D
ADDED
 
 
MiaB like protein
- very conserved; best matches 23k22 and 41b15 acidobacterial soil clones and Ellin345
PROTEIN
COG0621 2-methylthioadenine synthetase
J Translation, ribosomal structure and biogenesis
Good
 
82.227.62.180
10/09/07 22:44:16
 
 
LUAcid_AD106_G4_06
5978
4743
 
 
radical SAM domain protein
 
1
R
ADDED
 
 
radical SAM domain protein
- very conserved in bacteria - best match to acidobacterial soil clones 23k22 and 41b15 - conserved in tandem with MiaB like protein in Acidobacteria
PROTEIN
J Translation, ribosomal structure and biogenesis
 
Good
 
82.227.62.180
10/09/07 22:51:55
 
 
LUAcid_AD106_G4_07
6039
7292
 
 
putative protease
 
1
D
ADDED
 
 
putative protease
conserved in acidobacterial soil clone 23k22 and 41b15 with two adjacent proteins (057, 071, 082)
PROTEIN
COG0612 Predicted Zn-dependent peptidases
R General function prediction only
Good
 
82.227.62.180
10/09/07 22:58:43
 
 
LUAcid_AD106_G4_01
20
352
 
 
truncated hypothetical protein
 
1
D
ADDED
 
 
hypothetical protein
- best match to Aquifex - COG prediction suspect
PROTEIN
COG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfG
C Energy production and conversion
Good but overlapping
 
129.175.112.252
11/09/07 09:37:04
 
 
LUAcid_AD106_G4_08
7411
8238
 
 
beta-lactamase-like protein
 
1
D
ADDED
 
 
putative metallo-beta-lactamase family protein
 
PROTEIN
COG1235 Metal-dependent hydrolases of the beta-lactamase superfamily I
R General function prediction only
Good
 
129.175.112.252
11/09/07 09:44:21
 
 
L35480_AD106_G4_056
4636
4439
 
 
 
 
1
R
DELETED
 
 
 
 
 
 
 
-
 
129.175.105.75
11/09/07 10:08:11
 
 
L35480_AD106_G4_002
266
21
 
 
test
 
1
R
ADDED
 
 
 
test-comment
PROTEIN
COG0122 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase
L Replication, recombination and repair
-
 
129.175.105.75
11/09/07 13:32:43
 
 
L35480_AD106_G4_002
266
21
 
 
 
 
1
R
DELETED
 
 
 
 
 
 
 
-
 
129.175.105.75
11/09/07 16:59:13
 
 
LUAcid_AD106_G4_03
828
1835
 
 
ApbE-like lipoprotein
 
45
D
ADDED
 
 
 
- one match in Solibacter usitatus Ellin7606, not in A. bacterium Ellin345 - matches only bacteria, not archaea, not eukarya - best match with 31% identities - start codon changed after alignment (TTG to ATG at 45aa)
PROTEIN
COG1477 Membrane-associated lipoprotein involved in thiamine biosynthesis
H Coenzyme transport and metabolism
Good
 
82.227.62.180
11/09/07 18:46:02
 
 
LUAcid_AD106_G4_02
352
828
 
 
hypothetical transmembrane protein
 
1
D
ADDED
 
 
 
- no COG  - very low similarities - best match Ralstonia Rsc0621 protein considering length and cooccurence in Ralstonia with ApbE-like protein as here - after TMHMM scan: prediction of 4 TMhelices
PROTEIN
 
 
Good
 
82.227.62.180
11/09/07 20:08:29
 
 
LUAcid_AD106_G4_09
8245
9540
 
 
adenylosuccinate lyase (PurB)
 
1
D
ADDED
 
 
 
- very conserved - best match to acidobacterial clone 41b15 and 23k22 and A. bacterium Ellin345 - enzyme in purine ribonucleotide biosynthesis - calalytic reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP - length very good - cooccurence with beta lactamase domain protein in Solibacter usitatus Ellin6076 - equally here with ORF094
PROTEIN
COG0015 Adenylosuccinate lyase
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 20:32:48
 
 
LUAcid_AD106_G4_10
9546
9782
 
 
phosphoribosylformylglycinamidine  synthase I (PurS)
 
1
D
ADDED
 
 
 
- best match acidobacterial soil clones 23k22 and 41b15 containing gene cluster for purine ribonucleotide biosynthesis - length OK
PROTEIN
COG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 20:39:37
 
 
LUAcid_AD106_G4_11
9839
10552
 
 
phosphoribosylformylglycinamidine  synthase I (PurQ; FGAM synthase I)
 
1
D
ADDED
 
 
 
- best match acidobacterial soil clone 41b15 and 23k22 - 70% identity to 41b15 PurQ  - part of purin biosynthesis operon - length OK
PROTEIN
 
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 21:20:06
 
 
LUAcid_AD106_G4_12
10468
12798
 
 
phosphoribosylformylglycinamidine  synthase II (PurL)
 
31
D
ADDED
 
 
 
- best match to acidobacterial soil clone 23k22 and 41b15 - FGAM Synthase II - in purin biosynthesis operon - change of start codon to 31 (ATG)
PROTEIN
COG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 21:25:32
 
 
LUAcid_AD106_G4_13
12798
14249
 
 
amidophosphoribosyl transferase (PurF)
 
4
D
ADDED
 
 
 
- best match to acidobacterial soil clone 41b15 and 23k22 - purin biosynthesis operon - very conserved: 65% identity to PurF from 41b15 - change start codon to 4aa (ATG)
PROTEIN
COG0034 Glutamine phosphoribosylpyrophosphate amidotransferase
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 21:32:47
 
 
LUAcid_AD106_G4_14
14304
15395
 
 
phosphoribosylformylglycinamidine  cyclo ligase (PurM, AIR Synthetase)
 
1
D
ADDED
 
 
 
- best match to acidobacterial soil clones 23k22 and 41b15 - very conserved 63% identity to PurM of 23k22 - purin biosynthesis operon - PurM (Aminoimidazole Ribonucleotide [AIR] synthetase
PROTEIN
COG0150 Phosphoribosylaminoimidazole (AIR) synthetase
F Nucleotide transport and metabolism
Good but overlapping
 
82.227.62.180
11/09/07 21:37:59
 
 
LUAcid_AD106_G4_15
15456
16067
 
 
phosphoribosylglycinamide formyltransferase (PurN)
 
8
D
ADDED
 
 
 
- best match to acidobacterial soil clones 23k22 and 41b15 - purin biosynthesis operon - very conserved: 62% identiy - folate dependent enzyme - start codon change to 8aa (ATG), since first 10aa not conserved, choose of ATG instead of GTG
PROTEIN
COG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurN
F Nucleotide transport and metabolism
Good
 
82.227.62.180
11/09/07 21:50:56
 
 
LUAcid_AD106_G4_16
16067
17302
 
 
tyrosyl-tRNA synthetase (TyrS)
 
8
D
ADDED
 
 
 
- best match acidobacterial soil clone 23k22, then Solibacter and proteobacteria - very conserved: 52% identity to 23k22 - eventually phylogeny - change of start codon to 8aa, since overlap and comparison to other TyrS
PROTEIN
COG0162 Tyrosyl-tRNA synthetase
J Translation, ribosomal structure and biogenesis
Good
 
82.227.62.180
12/09/07 08:29:06
 
 
LUAcid_AD106_G4_18
25157
26686
 
 
conserved hypothetical protein
 
1
D
ADDED
 
 
 
- best match to Myxococcus xanthus 7198 - also good match to Ellin345 (ORF Acid2212) and Solibacter (Ellin 6706) ORF 2212 - homologs annotated as putative lipoprotein ? - InterPro: zinc metallopeptidase domain - no transmembrane domain - no COG hit - start codon OK
PROTEIN
 
 
Good
 
82.227.62.180
12/09/07 09:14:59
 
 
LUAcid_AD106_G4_19
26700
28145
 
 
FAD linked oxidase
 
12
D
ADDED
 
 
 
- best match Rubrobacter xylanophilus - very conserved 56% identity - D-lactat dehydrogenase (cytochrome) - FAD/FMN- containing dehydrogenase (GlcD) - start codon change to 12aa, to eluminate overlap and change from TTG to ATG
PROTEIN
COG0277 FAD/FMN-containing dehydrogenases
C Energy production and conversion
Good
 
82.227.62.180
12/09/07 16:23:11
 
 
LUAcid_AD106_G4_20
28167
29429
 
 
FAD linked oxidase-like protein (GlcE subunit ?)
 
1
D
ADDED
 
 
 
- best match to Rubrobacter xylanophilus (YP_645556.1) - very conserved 40% identity - together with 331 (best match to YP_645557.1) and 348 seems to be two subunits of Glycolate oxidase  - ORF348 subunit GlcE - ORF 331 and 348 in tandem also in Rubrobacter
PROTEIN
Energy
 
Good
 
82.227.62.180
12/09/07 16:36:45
 
 
LUAcid_AD106_G4_21
30834
29509
 
 
protein of unknown function DUF224
 
1
R
ADDED
 
 
 
 
PROTEIN
 
 
Good
 
82.227.62.180
12/09/07 17:47:25
 
 
LUAcid_AD106_G4_21
30834
29509
 
 
protein of unknown function DUF224
 
1
R
ADDED
 
 
 
- best match to Rubrobacter xylanophilus (Actinobacteria high GC gram+) (YP_645555.1)  (Glycolate oxidase subunit GlcF?) - very conserved 58% identity - together with 331 (best match to YP_645557.1) and 348 (YP_645556.1) seems to be three subunits of Glycolate oxidase - ORF348 subunit GlcE - ORF 331 and 348 and 363 also in Rubrobacter - match also in Solibacter, but low e-value, seems to be another protein - in general matches in all kind of bacteria 
PROTEIN
 
 
Good
 
82.227.62.180
12/09/07 17:48:06
 
 
LUAcid_AD106_G4_22
31005
32000
 
 
NADPH:quinone reductase and related Zn-dependent oxidoreductases
 
1
D
ADDED
 
 
 
- best match to Magnetospirillum magneticum ZP_00054546 - very conserved 56% identity - not present in soil clones - present in sequnces acidobacteria
PROTEIN
COG0604 NADPH:quinone reductase and related Zn-dependent oxidoreductases
C Energy production and conversion
Good
 
82.227.62.180
12/09/07 18:06:30
 
 
LUAcid_AD106_G4_23
32023
32481
 
 
Endoribonuclease L-PSP
 
35
D
ADDED
 
 
 
- best match to Ellin345 YP_593389.1 - change of start codon to 35aa - Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3] - could be involved in purin biosynthesis
PROTEIN
COG0024 Methionine aminopeptidase
J Translation, ribosomal structure and biogenesis
Good
 
82.227.62.180
12/09/07 18:16:08
 
 
LUAcid_AD106_G4_24
32492
34354
 
 
gamma-glutamyltranspeptidase
 
1
D
ADDED
 
 
 
- best match to Congregibacter litoralis KT71 - very conserved 53% identity - 7 homologs in Ellin345 - Gamma-glutamyltranspeptidase (GGT) catalyses the transfer of the glutathione  gamma-glutamyl moiety to an acceptor that may be an amino acid, a peptide  or water (forming glutamate) [1]. GGT plays a central role in glutathione  metabolism, and drug and xenobiotic detoxification [2]. In both prokaryotes and eukaryotes, the enzyme contains heavy and light subunits, which are  processed from a single chain precursor. The light subunit houses the GGT  active site.
PROTEIN
 
 
Good
 
82.227.62.180
12/09/07 18:41:29
 
 
LUAcid_AD106_G4_25
34360
34848
 
 
acetyltransferase (GNAT) family protein
 
4
D
ADDED
 
 
 
- best match to Desulfovibrio desulfuricans G20 - 39% identity - start codon changed to 4aa in accordance to length of homologs; but start codon also at 12aa
PROTEIN
COG0454 Histone acetyltransferase HPA2 and related acetyltransferases
K Transcription
Good
 
82.227.62.180
12/09/07 18:48:39
 
 
LUAcid_AD106_G4_26
35335
34865
 
 
hypothetical protein
 
11
R
ADDED
 
 
 
- best match to Salinibacter ruber - 32% identity - change of start codon to 11aa
PROTEIN
 
 
Good
 
82.227.62.180
12/09/07 18:52:19
 
 
LUAcid_AD106_G4_29
36272
37018
 
 
protein of unknown function DUF28
 
1
D
ADDED
 
 
 
- best matches to both Acidobacteria (Ellin345_2125); Ellin6706: Acid5948; 56% identity - present in clone KM3_47_B8_048 (ORF048) - more than 73% identity - conserved in all Bacteria, not in Archaea and Eukarya
PROTEIN
COG0217 Uncharacterized conserved protein
S Function unknown
Good
 
82.227.62.180
13/09/07 08:21:01
 
 
LUAcid_AD106_G4_30
37018
37569
 
 
crossover junction endodeoxyribonuclease RuvC
 
1
D
ADDED
 
 
 
- conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA),  RuvB (Holliday junction ATP-dependent DNA helicase ruvB) - syntheny conserved in other Bacteria with DUF28  - present in clone KM3_47_B8_039 (ORF39), region conserved (operon?) with DUF0028 and KM3_47_B8_032 (ORF32) and KM3_47_B8_026 (ORF26), same as here with ORF452 (Holliday junction DNA helicase RuvA) and ORF467 RuvB - best match to Ellin345_3618; 48%identity and to clone KM3_47_B8_39; 57% identity 
PROTEIN
COG0817 Holliday junction resolvasome, endonuclease subunit
L Replication, recombination and repair
-
 
82.227.62.180
13/09/07 09:23:07
 
 
LUAcid_AD106_G4_31
37575
38174
 
 
Holliday junction DNA helicase RuvA
 
1
D
ADDED
 
 
 
- conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA),  RuvB (Holliday junction ATP-dependent DNA helicase ruvB)  
PROTEIN
COG0632 Holliday junction resolvasome, DNA-binding subunit
L Replication, recombination and repair
Good
 
82.227.62.180
13/09/07 09:39:27
 
 
LUAcid_AD106_G4_32
38183
39199
 
 
Holliday junction DNA helicase RuvB
 
1
D
ADDED
 
 
 
- best match to Acid_4544 58% identity and Acid_0957 - match also to KM3_47_B8_026, but sequence in this clone very short, must be verified
PROTEIN
COG2255 Holliday junction resolvasome, helicase subunit
L Replication, recombination and repair
Good
 
82.227.62.180
13/09/07 09:47:56
 
 
LUAcid_AD106_G4_33
39321
40307
 
 
3-oxoacyl-(acyl-carrier-protein) synthase III
 
15
D
ADDED
 
 
 
- best match Solibacter usitatus Ellin6076 Acid_7048 and Ellin345 Acid345_2017, 61% identities - not in other clones
PROTEIN
COG0332 3-oxoacyl-[acyl-carrier-protein] synthase III
I Lipid transport and metabolism
Good
 
82.227.62.180
13/09/07 10:17:09
 
 
LUAcid_AD106_G4_34
40350
41399
 
 
S-adenosylmethionine:tRNA ribosyltransferase-isomerase
 
1
D
ADDED
 
 
 
- best match Geobacillus 48% identity - very conserved in Bacteria, not in A and E - not in other clones - lower matches in Ellin345 and Ellin6706
PROTEIN
COG0809 S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase)
J Translation, ribosomal structure and biogenesis
Good
 
82.227.62.180
13/09/07 10:25:22
 
 
LUAcid_AD106_G4_27
35386
35817
 
 
hypothetical protein
 
20
D
ADDED
 
 
 
- SAM binding motif - Methyltransferase type 11 motif - but low similarity - change of start codon to 20aa because of overlap
PROTEIN
 
 
Good
 
82.227.62.180
13/09/07 10:30:15
 
 
LUAcid_AD106_G4_28
35813
36151
 
 
hypothetical protein
 
1
D
ADDED
 
 
 
- very low similarity - length not corresponding - InterPro: Methyltransferase as ORF430 perhaps frameshift and 430+433 corresponds to one gene
PROTEIN
 
 
Good
 
82.227.62.180
13/09/07 11:02:42
 
 
LUAcid_AD106_G4_35
41828
41487
 
 
hypothetical protein
 
1
R
ADDED
 
 
 
- low similarity - domain: Ribonuclease H-like - but ORF too short - transposase similarity - integrase, calatytic region match - helix-turn-helix Fis type match
PROTEIN
 
 
-
 
82.227.62.180
13/09/07 11:12:05
 
 
L35480_AD106_G4_002
266
21
 
 
 
 
1
R
DELETED
 
 
 
 
 
 
 
-
 
129.175.105.75
13/09/07 18:45:09
 
 
LUAcid_AD106_G4_08
7411
8238
 
 
beta-lactamase-like protein
 
1
D
ADDED
 
 
 
- Clostridium thermocellum ATCC 27405 (36% id) - also COG0324 - seems to be part of purin operon
PROTEIN
COG1235 Metal-dependent hydrolases of the beta-lactamase superfamily I
R General function prediction only
Good
 
82.227.62.180
18/09/07 09:20:37
- paralogs on different clones LUAcid_KM3_G1_01 LUAcid_KM3_D9_13 LUAcid_AD106_G4_08 L35498_AD55_D2_360 LUAcid_KM4_H7_24
 
LUAcid_AD106_G4_09
8245
9540
 
 
adenylosuccinate lyase (PurB)
 
1
D
ADDED
 
 
 
- best match to KM3_187_G1_032 (68% id) - next match 23k22 (65% id) - purine ribonucleotide biosynthetic process
PROTEIN
COG0015 Adenylosuccinate lyase
F Nucleotide transport and metabolism
Good
ABE
82.227.62.180
18/09/07 11:30:22
- orthologs found in other clones: LUAcid_KM3_G1_02 LUAcid_KM3_D9_14 L35498_AD55_D2_353  LUAcid_AD106_G4_09 LUAcid_KM4_H7_25 23k22_016 PurB (AY281356 soil clone) 41b15_012 PurB (AY281352 soil clone)
 
LUAcid_AD106_G4_10
9546
9782
 
 
phosphoribosylformylglycinamidine synthase I (PurS)
 
1
D
ADDED
 
 
 
- best match to KM3_205_D9_268 (70% id) - purin biosynthesis pathway
PROTEIN
COG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component
F Nucleotide transport and metabolism
Good
AB
82.227.62.180
18/09/07 11:46:31
- orthologs on other acidobacterial clones: LUAcid_KM3_G1_03 L35498_AD55_D2_340 LUAcid_KM3_D9_15 LUAcid_AD106_G4_10  LUAcid_KM4_H7_26 23k22_011 PurS AY281352 41b15_015 PurS AY281356
 
LUAcid_AD106_G4_11
9839
10552
 
 
phosphoribosylformylglycinamidine synthase I (PurQ)
 
1
D
ADDED
 
 
 
best match to KM3_205_D9_262 (84% id) - Purin biosynthesis operon
PROTEIN
COG0047 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain
F Nucleotide transport and metabolism
Good
AB
82.227.62.180
18/09/07 13:08:57
- several orthologs in Acidobacteria LUAcid_KM3_G1_04 LUAcid_KM3_D9_16 L35498_AD55_D2_336 LUAcid_AD106_G4_11 LUAcid_KM4_H7_27 41b15_014 PurQ AY281356 23k22_010 PurQ AY281352 Acid345_2235  Acid_5943
 
LUAcid_AD106_G4_12
10468
12798
 
 
phosphoribosylformylglycinamidine synthase II (PurL)
 
1
D
ADDED
 
6.3.5.3
 
best match to KM3_205_D9_254 (77% id) - purin biosynthesis operon - AIR synthase related protein - ’de novo’ IMP biosynthetic process - hosphoribosylformylglycinamidine synthase is a single, long polypeptide in most bacteria. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II.
PROTEIN
COG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain
F Nucleotide transport and metabolism
Good
AB
82.227.62.180
18/09/07 13:58:19
several orthologs in Acidobacteria: LUAcid_KM3_G1_06 LUAcid_KM3_D9_17 L35498_AD55_D2_328 LUAcid_AD106_G4_12 LUAcid_KM4_H7_28 L35511_KM3_47_B8_428 23k22_009 PurL AY281352 41b15_013 PurL AY281356 Acid_5944 Acid345_4622
 
LUAcid_AD106_G4_13
12798
14249
 
 
amidophosphoribosyl transferase (PurF)
 
1
D
ADDED
 
2.4.2.14
 
- best match to KM3_205_D9_226 (78% id) - purin biosynthesis operon - also COG0449 - Purine nucleotides are synthesised both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. Amidophosphoribosyltransferase (EC:2.4.2.14) is the rate-limiting enzyme in the de novo pathway of purine ribonucleotide synthesis and is regulated by feedback inhibition by AMP and GMP [1].
PROTEIN
COG0034 Glutamine phosphoribosylpyrophosphate amidotransferase
F Nucleotide transport and metabolism
Good
ABE
82.227.62.180
18/09/07 16:23:38
several othologs in Acidobacteria LUAcid_KM3_G1_07 LUAcid_KM3_D9_18 L35511_KM3_47_B8_405 L35498_AD55_D2_302 LUAcid_AD106_G4_13 LUAcid_KM4_H7_29 41b15_012 PurF AY281356 23k22_008 PurF AY281352 Acid345_4621 Acid_5945
 
LUAcid_AD106_G4_01
20
352
 
 
truncated hypothetical protein
 
1
D
ADDED
 
 
hypothetical protein
- best match to Aquifex - COG prediction suspect
PROTEIN
COG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfG
C Energy production and conversion
Good but overlapping
 
82.227.62.180
1/10/07 11:15:31
- good partial match to KM3_205_D9_412 and 373 - doimain pattern: B
 
LUACID_AD106_G4_17
24163
24933
 
 
hypothetical protein
 
1
D
ADDED
 
 
hypothetical protein
one single match in Ellin345
PROTEIN
 
 
Good
 
82.227.62.180
8/10/07 15:26:15
conserved only in deep sea acidobacterial clones: AD106_G4_17 KM3_A5_18   KM3_D9_23   KM3_G1_12   KM3_B8D2_15 Acid345_1727, not Solibacter - overall identity with 6 sequences >40% --> very conserved - domain pattern - unique for deep sea
 
LUACID_AD106_G4_18
25157
26686
 
 
conserved hypothetical protein
 
1
D
ADDED
 
 
 
- best match to Myxococcus xanthus 7198 - also good match to Ellin345 (ORF Acid2212) and Solibacter (Ellin 6706) ORF 2212 - homologs annotated as putative lipoprotein ? - InterPro: zinc metallopeptidase domain - no transmembrane domain - no COG hit - start codon OK
PROTEIN
 
 
Good
 
82.227.62.180
8/10/07 15:39:14
- very conserved in acidobacteria; 5 matches in deep sea clones, no matches in soil clones, one match in each genome, matches also in other bacteria AD106_G4_18  KM3_G1_13    KM3_D9_25    KM3_B8D2_17  KM3_A5_19    ACID345_3935 ACID_2212    
 
LUACID_AD106_G4_16SRNA
17717
19275
 
 
16S ribosomal RNA
 
1
D
ADDED
16SrRNA
 
 
 
RNA
 
 
 
 
129.175.105.75
29/10/07 17:21:32
 
 
LUACID_AD106_G4_23SRNA
20415
23302
 
 
23S ribosomal RNA
 
1
D
ADDED
23SrRNA
 
 
 
RNA
 
 
 
 
129.175.105.75
29/10/07 17:22:33
 
 
LUACID_AD106_G4_5SRNA
23650
23774
 
 
5S ribosomal RNA
 
1
D
ADDED
5SrRNA
 
 
 
RNA
 
 
 
 
129.175.105.75
29/10/07 17:23:44
 
 
LUACID_AD106_G4_TRNA1
19520
19593
 
 
tRNA-Ile (GAT)
 
1
D
ADDED
tRNA-Ile
 
 
 
TRNA
 
 
 
 
129.175.105.75
29/10/07 17:26:27
 
 
LUACID_AD106_G4_TRNA2
20009
20081
 
 
tRNA-Ala (TGC)
 
1
D
ADDED
tRNA-Ala
 
 
 
TRNA
 
 
 
 
129.175.105.75
29/10/07 17:27:07
 
 
LUACID_AD106_G4_TRNA3
41442
41515
 
 
tRNA-Met (CAT)
 
1
D
ADDED
tRNA-Met
 
 
 
TRNA
 
 
 
 
129.175.105.75
29/10/07 17:28:00
 
 
LUACID_AD106_G4_06
5978
4743
 
 
radical SAM domain protein
 
1
R
ADDED
 
 
 
- very conserved in bacteria - best match to acidobacterial soil clones 23k22 and 41b15 - conserved in tandem with MiaB like protein in Acidobacteria
PROTEIN
COG0820 Predicted Fe-S-cluster redox enzyme
R General function prediction only
Good
B
129.175.105.75
17/12/07 14:37:25
fixed COG -yz
 
LUACID_AD106_G4_21
30834
29509
 
 
Glycolate oxidase, iron-sulphur subunit
 
1
R
ADDED
glcF
 
 
- best match to Rubrobacter xylanophilus (Actinobacteria high GC gram+) (YP_645555.1) (Glycolate oxidase subunit GlcF?) - very conserved 58% identity - together with 331 (best match to YP_645557.1) and 348 (YP_645556.1) seems to be three subunits of Glycolate oxidase - ORF348 subunit GlcE - ORF 331 and 348 and 363 also in Rubrobacter - match also in Solibacter, but low e-value, seems to be another protein - in general matches in all kind of bacteria
PROTEIN
COG0247 Fe-S oxidoreductase
C Energy production and conversion
Good
B
129.175.105.75
17/12/07 14:53:57
fixed def/cog/gN -yz
 
LUACID_AD106_G4_24
32492
34354
 
 
gamma-glutamyltranspeptidase
 
1
D
ADDED
ggt
2.3.2.2
 
- best match to Congregibacter litoralis KT71 - very conserved 53% identity - 7 homologs in Ellin345 - Gamma-glutamyltranspeptidase (GGT) catalyses the transfer of the glutathione gamma-glutamyl moiety to an acceptor that may be an amino acid, a peptide or water (forming glutamate) [1]. GGT plays a central role in glutathione metabolism, and drug and xenobiotic detoxification [2]. In both prokaryotes and eukaryotes, the enzyme contains heavy and light subunits, which are processed from a single chain precursor. The light subunit houses the GGT active site.
PROTEIN
COG0405 Gamma-glutamyltransferase
E Amino acid transport and metabolism
Good
 
129.175.105.75
17/12/07 15:09:10
fixed EC/gN/COG -yz
 
LUACID_AD106_G4_35
41828
41487
 
 
hypothetical protein
 
1
R
ADDED
 
 
 
- low similarity - domain: Ribonuclease H-like - but ORF too short - transposase similarity - integrase, calatytic region match - helix-turn-helix Fis type match
PROTEIN
COG2801 Transposase and inactivated derivatives
L Replication, recombination and repair
-
 
129.175.105.75
17/12/07 15:59:31
 
 
LUACID_AD106_G4_01
20
352
 
 
truncated hypothetical protein
 
1
D
ADDED
 
 
 
- best match to Aquifex - COG prediction suspect
PROTEIN
 
 
Good but overlapping
 
129.175.105.75
17/12/07 17:17:51
fixed COG -yz
 
LUACID_AD106_G4_05
3372
4736
 
 
MiaB like protein tRNA modifiying enzyme
 
1
D
ADDED
MiaB-like
 
 
- very conserved; best matches 23k22 and 41b15 acidobacterial soil clones and Ellin345
PROTEIN
COG0621 2-methylthioadenine synthetase
J Translation, ribosomal structure and biogenesis
Good
 
129.175.105.75
30/01/08 17:19:09
 
 
LUACID_AD106_G4_09
8245
9540
 
 
adenylosuccinate lyase (PurB)
 
1
D
ADDED
PurB
 
 
- best match to KM3_187_G1_032 (68% id) - next match 23k22 (65% id) - purine ribonucleotide biosynthetic process
PROTEIN
COG0015 Adenylosuccinate lyase
F Nucleotide transport and metabolism
Good
ABE
129.175.105.75
30/01/08 17:33:39
- orthologs found in other clones: LUAcid_KM3_G1_02 LUAcid_KM3_D9_14 L35498_AD55_D2_353  LUAcid_AD106_G4_09 LUAcid_KM4_H7_25 23k22_016 PurB (AY281356 soil clone) 41b15_012 PurB (AY281352 soil clone)
 
LUACID_AD106_G4_10
9546
9782
 
 
phosphoribosylformylglycinamidine synthase I (PurS)
 
1
D
ADDED
PurS
 
 
- best match to KM3_205_D9_268 (70% id) - purin biosynthesis pathway
PROTEIN
COG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component
F Nucleotide transport and metabolism
Good
AB
129.175.105.75
30/01/08 17:35:18
- orthologs on other acidobacterial clones: LUAcid_KM3_G1_03 L35498_AD55_D2_340 LUAcid_KM3_D9_15 LUAcid_AD106_G4_10  LUAcid_KM4_H7_26 23k22_011 PurS AY281352 41b15_015 PurS AY281356
 
LUACID_AD106_G4_11
9839
10552
 
 
phosphoribosylformylglycinamidine synthase I (PurQ)
 
1
D
ADDED
PurQ
 
 
best match to KM3_205_D9_262 (84% id) - Purin biosynthesis operon
PROTEIN
COG0047 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain
F Nucleotide transport and metabolism
Good
AB
129.175.105.75
30/01/08 17:36:07
- several orthologs in Acidobacteria LUAcid_KM3_G1_04 LUAcid_KM3_D9_16 L35498_AD55_D2_336 LUAcid_AD106_G4_11 LUAcid_KM4_H7_27 41b15_014 PurQ AY281356 23k22_010 PurQ AY281352 Acid345_2235  Acid_5943
 
LUACID_AD106_G4_12
10558
12798
 
 
phosphoribosylformylglycinamidine synthase II (PurL)
 
1
D
ADDED
PurL
6.3.5.3
 
best match to KM3_205_D9_254 (77% id) - purin biosynthesis operon - AIR synthase related protein - Ġde novoĠ IMP biosynthetic process - hosphoribosylformylglycinamidine synthase is a single, long polypeptide in most bacteria. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II.
PROTEIN
COG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain
F Nucleotide transport and metabolism
Good
AB
129.175.105.75
30/01/08 17:37:12
several orthologs in Acidobacteria: LUAcid_KM3_G1_06 LUAcid_KM3_D9_17 L35498_AD55_D2_328 LUAcid_AD106_G4_12 LUAcid_KM4_H7_28 L35511_KM3_47_B8_428 23k22_009 PurL AY281352 41b15_013 PurL AY281356 Acid_5944 Acid345_4622
 
LUACID_AD106_G4_13
12807
14249
 
 
amidophosphoribosyl transferase (PurF)
 
1
D
ADDED
PurF
2.4.2.14
 
- best match to KM3_205_D9_226 (78% id) - purin biosynthesis operon - also COG0449 - Purine nucleotides are synthesised both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. Amidophosphoribosyltransferase (EC:2.4.2.14) is the rate-limiting enzyme in the de novo pathway of purine ribonucleotide synthesis and is regulated by feedback inhibition by AMP and GMP [1].
PROTEIN
COG0034 Glutamine phosphoribosylpyrophosphate amidotransferase
F Nucleotide transport and metabolism
Good
ABE
129.175.105.75
30/01/08 17:39:54
several othologs in Acidobacteria LUAcid_KM3_G1_07 LUAcid_KM3_D9_18 L35511_KM3_47_B8_405 L35498_AD55_D2_302 LUAcid_AD106_G4_13 LUAcid_KM4_H7_29 41b15_012 PurF AY281356 23k22_008 PurF AY281352 Acid345_4621 Acid_5945
 
LUACID_AD106_G4_14
14304
15395
 
 
phosphoribosylformylglycinamidine  cyclo ligase (PurM, AIR Synthetase)
 
1
D
ADDED
PurM
 
 
- best match to acidobacterial soil clones 23k22 and 41b15 - very conserved 63% identity to PurM of 23k22 - purin biosynthesis operon - PurM (Aminoimidazole Ribonucleotide [AIR] synthetase
PROTEIN
COG0150 Phosphoribosylaminoimidazole (AIR) synthetase
F Nucleotide transport and metabolism
Good but overlapping
 
129.175.105.75
30/01/08 17:41:58
 
 
LUACID_AD106_G4_15
15456
16067
 
 
phosphoribosylglycinamide formyltransferase (PurN)
 
8
D
ADDED
PurN
 
 
- best match to acidobacterial soil clones 23k22 and 41b15 - purin biosynthesis operon - very conserved: 62% identiy - folate dependent enzyme - start codon change to 8aa (ATG), since first 10aa not conserved, choose of ATG instead of GTG
PROTEIN
COG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurN
F Nucleotide transport and metabolism
Good
 
129.175.105.75
30/01/08 17:42:24
 
 
LUACID_AD106_G4_16
16067
17302
 
 
tyrosyl-tRNA synthetase (TyrS)
 
8
D
ADDED
TyrS
 
 
- best match acidobacterial soil clone 23k22, then Solibacter and proteobacteria - very conserved: 52% identity to 23k22 - eventually phylogeny - change of start codon to 8aa, since overlap and comparison to other TyrS
PROTEIN
COG0162 Tyrosyl-tRNA synthetase
J Translation, ribosomal structure and biogenesis
Good
 
129.175.105.75
30/01/08 17:42:47
 
 
LUACID_AD106_G4_30
37018
37569
 
 
crossover junction endodeoxyribonuclease RuvC
 
1
D
ADDED
RuvC
 
 
- conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA),  RuvB (Holliday junction ATP-dependent DNA helicase ruvB) - syntheny conserved in other Bacteria with DUF28  - present in clone KM3_47_B8_039 (ORF39), region conserved (operon?) with DUF0028 and KM3_47_B8_032 (ORF32) and KM3_47_B8_026 (ORF26), same as here with ORF452 (Holliday junction DNA helicase RuvA) and ORF467 RuvB - best match to Ellin345_3618; 48%identity and to clone KM3_47_B8_39; 57% identity
PROTEIN
COG0817 Holliday junction resolvasome, endonuclease subunit
L Replication, recombination and repair
-
 
129.175.105.75
30/01/08 17:43:29
 
 
LUACID_AD106_G4_31
37575
38174
 
 
Holliday junction DNA helicase RuvA
 
1
D
ADDED
RuvA
 
 
- conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA),  RuvB (Holliday junction ATP-dependent DNA helicase ruvB)
PROTEIN
COG0632 Holliday junction resolvasome, DNA-binding subunit
L Replication, recombination and repair
Good
 
129.175.105.75
30/01/08 17:43:59
 
 
LUACID_AD106_G4_32
38183
39199
 
 
Holliday junction DNA helicase RuvB
 
1
D
ADDED
RuvB
 
 
- best match to Acid_4544 58% identity and Acid_0957 - match also to KM3_47_B8_026, but sequence in this clone very short, must be verified
PROTEIN
COG2255 Holliday junction resolvasome, helicase subunit
L Replication, recombination and repair
Good
 
129.175.105.75
30/01/08 17:44:22