TABLE 4.

RQ2-specific sequences with significant protein matches in The Institute for Genomic Research and/or The National Center for Biotechnology Information protein databases

Group and cloneabpbFirst BLASTX hitcOrganismExpect value% IdentitydNote
Transporters
    2D4210TM0114 sugar ABC transporterT. maritima MSB83.9E−0438TM0114 also among divergent clones
    TAD66
    KJ3D83277.7E−2648
    TAB05
    TAF50225TM0115 sugar ABC transporterT. maritima MSB85.5E−1958
    TAA05584a, TM0115 sugar ABC transporterT. maritima MSB87.0E−2250In T. neapolitana, sequence b is linked to XloA in C6
b, mannosidaseThermotoga neapolitana1.0E-104 (DNA)100 (DNA)
    TAB16215TM0430 sugar ABC transporterT. maritima MSB85.5E−1652
    TXX1
    2H5197TM0432 sugar ABC transporterT. maritima MSB82.7E−2080
    TAA71
    TAE94430TM0595 sugar ABC transporterT. maritima MSB81.0E−433
    2A2335TM0955 ribose ABC transporterT. maritima MSB84.1E−2067
    TAD76263TM1066 oligopeptide ABC transporterT. maritima MSB83.0E−2679Probably two different loci; TM1066 is also represented among the divergent clones
    TAE321671.0E−2074
    TAE41466TM1067 oligopeptide ABC transporterT. maritima MSB87.6E−1064
    TAE801728.2E−1144
    TAD15561TM1854 sugar ABC transporterT. maritima MSB82.0E−1039Start of clone shows no similarity
    3A4220Hypothetical sugar ABC-transporter geneAgrobacterium rhizogenes1.0E−1452
    4E9
    TAB60632Ribose ABC transporterLactococcus lactis1.0E−3168
    2A1354Bifunctional carbohydrate binding and transport proteinStreptomyces coelicolor A32.0E−0850
    TAC781805.0E−0760
    TAC69170Galactoside ABC transporterVibrio cholerae2.0E-06 (DNA)60 (DNA)
    TAE46237Lactose transport system permease proteinSynechocystis sp.5.0E−0432
    3F3500ABC transporter, periplasmic substrate-binding proteinDeinococcus radiodurans3.0E−4447RQ2 sequence cluster with Bacillus halodurans homolog in phylogenetic trees; also found in T. neapolitana, linked to clone E6
    TAC205671.0E−4447
    TAC08461Sugar transporter sugar binding proteinMesorhizobium loti1.0E−0729
    TXX3612Probable membrane transport proteinClostridium perfringens3.0E−2032
Degradation of polysaccharides
    C6198Thermotoga neapolitana xylosidase (XloA) and TM0076 xylosidaseThermotoga neapolitana, T. maritima MSB86.0E−1863Most likely two copies of this gene, B1 and 2A11, show 93% identity to T. neapolitana gene in DNA searches
    TAF78
    B14305.0E-61 (DNA)93 (DNA)
    2A11
    AE284921.0E−2669
    E6     TAF85723β-Glucosidase (bglA)T. maritima MSB8098Not reported in genome; see accession no. S34570; linked to clone 3F3
    KJ3B6457Family 10 xylanase gene xynCThermotoga sp. strain FjSS3-B.11.0E−92 (DNA)89 (DNA)Last 50 bp match noncoding region between TM1270 and TM1271 in T. maritima MSB8
    TAA59
    TAA425310 (DNA)95 (DNA)
    A8354BH1878—unknown conserved protein (781 aa)Bacillus halodurans2.0E−2155PSI BLAST searches suggest that BH1878 is an arabinosidase
    A124048.0E−1640
    TAE65
    TAE79There are at least 2 copies of this gene in the RQ2 genome
    C11853.0E−754
    TAF19
    TAA191146.0E−0460There also appear to be rearrangements compared to BH1878; the clones also show similarity to an arabinan endo-1,5-α-l-arabinosidase homolog (yxiA from Bacillus subtilis
    TAB072513.0E−2766
    TAC446266.0E−2644
    TAC835331.0E-0940
    TAE112401.0E-0840
    TAE302411.0E−0443
    KJ3D1292a, TM0280 hypothetical proteina, T. maritima MSB81.0E−14 (DNA)94 (DNA)Sequence a covers the end of TM0280; in T. maritima MSB8, TM0281 is an arabinosidase
    b, BH1878—unknown conserved protein (781 aa)b, Bacillus halodurans0.94 (DNA)67 (DNA)/PICK>
    KJ3B9248Hypothetical 52.5-kDa protein in hutP-bglP intergenic regionBacillus subtilis1.0E−0341Second hit, BH1878—unknown conserved protein
    TAA52565Arabinan endo-1,5-α-l-arabinosidaseBacillus subtilis2.0E−6664Second hit, BH1878—unknown conserved protein; two different copies of the gene
    TAF055333.5E−2968
    TAF151512.0E−1165
    KJB3521ArabinosidaseBacteroides ovatus3.0E−2337KJB3, TXX2, TAE82, and TAD18 may be from the same gene
    TXX24835.0E−4853
    TAE82297α-Arabinofuranosidase IStreptomyces chartreusis3.0E−0330
    TAD18505a, sugar ABC transportera, Listeria innocua6.0E−1343
    b, probable secreted arbinosidaseb, Streptomyces coelicolor5.0E−0956
    TAC01493β-XylosidaseClostridium acetobutylicum1.0E−1734Encoded on plasmid pSOL1 in C. acetobutylicum
    2A10568Pectin methylesterase-like proteinPectobacterium chrysanthemi7.0E−2040RQ2 clusters with Pectobacterium chrysanthemi in phylogenetic trees
    2A5
    KJ3D6
    TAC873544.0E−2050
Surface polysaccharides
    TAF75411dTDP-l-rhamnose synthase, rmlD geneLactococcus lactis1.8E−07 (DNA)58 (DNA)
    E9444dTDP-4-dehydrorhamnose 3,5-epimerase, rmlC geneShigella flexneri3.0E−3859
    2A4
    TAA18397dTDP-6-deoxy-d-glucose-3,5-epimerase, rmlC geneSalmonella enterica2.0E−1062Identical to E9 for bp 1-277
    TAA12320dTDP-glucose 4,6-dehydratase, rmlB geneMethanobacterium thermoautotrophicum8.0E−2768
    TAE89
    TAC74313Glucose-1-phosphate thymidylyltransferase rmlA geneSalmonella enterica2.0E−2559
    TAA67539Rhamnosyltransferase, wbaQ geneDeinococcus radiodurans7.0E−1236Might be a pseudogene frameshift at aa 73; no similarity after aa 83
    KJ3D12757Type 2 capsule locusStreptococcus pneumoniae6.0E−0325Similar to Wzx, flippase
    TAC91443a, spore coat polysaccharide synthesis, SpsKBacillus subtilis1.0E−0550Second hit of sequence a, RmlD from Listeria monocytogenes
b, TM0522 heat shock protein HslUT. maritima MSB81.4E−33 (DNA)94 (DNA)TM0522 and TM0523 rearranged, fused
c, TM0523 hypothetical proteinT. maritima MSB85.6E−12 (DNA)98 (DNA)
    TAF39209EpsF, WbnE putative glycosyl transferaseStreptococcus thermophilus2.0E−1361
Other
    A11367V-ATPase C subunitPyrococcus horikoshii2.0E−0130
    TAD64
    2B5765a, V-ATPase E subunitDesulfurococcus sp. strain SY3.927
    b, V-ATPase A subunitMethanobacterium thermoautotrophicum2.0E−0946
    KJ3D4309V-ATPase A subunitTreponema pallidum1.0E−4076
    TAB56491V-ATPase A subunitArchaeoglobus fulgidus5.0E−4455
    TAC60106V-ATPase A subunitDesulfurococcus mobilis1.0E−1091
    TAB82581V-ATPase E subunitDesulfurococcus sp. strain SY3.924
    5A12658V-ATPase F subunitTreponema pallidum2.0E−0328400 last bp of clone have no similarity
    KJB7321V-ATPase D subunitPyrococcus horikoshii1.0E−1235
    3A1
    4E10
    KJ2B4354V-ATPase 1 subunitHalobacterium sp. strain NRC-10.6224Not significant but included since a complete V-type operon is likely
    5A11525V-ATPase B subunitSulfolobus solfataricus5.0E−6262
    D5879MutS-like ATPase involved in mismatch repairThermoplasma volcanium2.0E−4637Phylogenetic analyses suggest that this gene belongs to a third group of prokaryote mutS homologs (Fig. 3)
    TAC191744.0E−0537
    TAF092551.0E−1955
    TAD435272.0E−1733
    TAA79305TM0758 flagellinT. maritima MSB81.0E−0738
    A5733TM0037 conserved hypothetical proteinT. maritima MSB82.5E−0431
    TAD45
    TAA71195TM0432 hypothetical proteinT. maritima MSB81.0E−2275
    TAE29738TM0619 conserved hypothetical proteinT. maritima MSB81.8E−2164
    TAC72307TM0941 hypothetical proteinT. maritima MSB82.0E−2450
    B11574a, TM0945 hypothetical proteinT. maritima MSB81.6E−075491-415, no hit; TM0946 deleted?
    TAC95b, TM0947 hypothetical protein6.0E−0463
    TAA68234Hypothetical proteinThermotoga neapolitana1.0E−106 (DNA)99
    TAF74682a, hypothetical protein YtaPBacillus subtilis1.0E−1129
    b, TM0076 xylosidaseT. maritima MSB84.0E−04 (DNA)81 (DNA)
    2B8489Long-chain primary alcohol dehydrogenaseThermoanaerobacter ethanolicus6.0E−4357RQ2 clusters with Thermoanaerobacter ethanolicus, Thermococcus hydrothermalis, and Giardia intestinalis to exclusion of T. maritima MSB8 homologs TM0111, TM0820, and TM0920
    TAB193021.0E−3370
    TAD491023.5E−0248
    KJ3C6191
    2A64891-PhosphofructokinasePseudomonas aeruginosa8.0E−2137RQ2 sequence and T. maritima MSB8 homolog TM0828 separated in phylogenetic tree
    KJ3D10749Hypothetical proteinAquifex aeolicus4.5E−0228
    2C2250Alkaline phosphataseSynechocystis sp.3.0E−0335
    TAD30726Immunoglobulin A-specific serine endopeptidaseNeisseria meningitidis3.0E−0325
    E11450a, TM1044 transposase, IS605-TnpB familyT. maritima MSB83.2E−15 (DNA)95 (DNA)BLASTX with sequence b: TM0972 conserved hypothetical protein, GGDEF domain
    TAD44b, conserved hypothetical protein aq_035Aquifex aeolicus1.0E−06 (DNA)59 (DNA)
    TAB30250Hypothetical protein PH0104Pyrococcus horikoshii2.0E−0331
    TAC56410Hypothetical protein PH0976Pyrococcus horikoshii7.0E−2140
    E2651a, MTH323 hypothetical proteinMethanobacterium thermoautotrophicum1.0E−0445
    2C12b, MTH324 hypothetical protein7.0E−0531
    TAC62464Hypothetical protein MTH328Methanobacterium thermoautotrophicum1.0E−0339
    TAF14363Hypothetical protein MTH296Methanobacterium thermoautotrophicum4.0E−0829
    TAD42708Integrin alpha chain, alpha 6Homo sapiens1.4E−0223
    B5212Methyl-accepting chemotaxis proteinPyrococcus abyssi7.0E−745Probably from the same gene
    TAD52221Clostridium acetobutylicum3.0E−740
  • a Clones starting with T were sequenced at The Institute for Genomic Research; the remaining clones were sequenced at Dalhousie University.

  • b For identical clones, the length is given for the first clone listed.

  • c If more than one gene was covered by the clone, they are given as follows: a, gene X; b, gene Y; c, gene Z.

  • d Percent identity refers to protein identity if not otherwise noted.

  • e aa, amino acids.