Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 188 bits (478), Expect = 2e-52 Identities = 98/241 (40%), Positives = 153/241 (63%), Gaps = 4/241 (1%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 PL++M+GI K FG+ +AL+ + + + PGE H L+G+NGAGKST +K +SGVH P +G+IL Sbjct: 9 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 68 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +G+P+ DP + AAGI ++Q LA+ P +SV+ N FMG+E ++G L DH Sbjct: 69 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLG---LIDHAAMR 125 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 T +R++G D A G LS E+Q V IARA+ ++++I+DEPT+AL R+T Sbjct: 126 SRTDAVLRQLGAGFGASDLA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 184 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 + + ++R +G+A+++I+H + A+ DR TVL G +G R +I +E + MM Sbjct: 185 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 244 Query: 246 G 246 G Sbjct: 245 G 245 Score = 100 bits (248), Expect = 8e-26 Identities = 71/229 (31%), Positives = 109/229 (47%), Gaps = 10/229 (4%) Query: 20 VIALAG-----VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFA 74 V ALAG S DV GE G GAG++ + + G + GDIL EG+P+H Sbjct: 271 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 330 Query: 75 DPRDAIAAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEE 131 PR A+ AGIA V + + M+V+ N M + L L + Sbjct: 331 QPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN--VASRHTRLGLVRSRSLGGVARAA 388 Query: 132 MRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATI 191 ++++ + + P+ VG LSGG +Q V +AR + KVLILDEPT + + + + + Sbjct: 389 IQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLV 448 Query: 192 DKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 ++ QGVAVV I+ + + + DR V+ G G I+ E + Sbjct: 449 HRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENI 497 Lambda K H 0.321 0.137 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 319 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 261 Length of database: 502 Length adjustment: 29 Effective length of query: 232 Effective length of database: 473 Effective search space: 109736 Effective search space used: 109736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory