Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_082353390.1 CDES_RS05835 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_001277995.1:WP_082353390.1 Length = 523 Score = 158 bits (399), Expect = 3e-43 Identities = 89/241 (36%), Positives = 143/241 (59%), Gaps = 6/241 (2%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 P++++ + K FG V + VS+DV PG LLG+NGAGKST IK MSGV++P G IL Sbjct: 14 PVLQLDRVSKSFGPVNVINQVSIDVRPGRVLALLGENGAGKSTLIKMMSGVYQPDGGQIL 73 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +G+P D + A A GIAT+HQ L ++P M+V+ N +G P RK G + + + Sbjct: 74 VDGKPTELPDTKAAEALGIATIHQELNLVPTMTVAENVMLGRTP-RKFG---MVNFKHLR 129 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 R + +G+++ + VG+L +Q V IA+A+ A++LILDEPT+AL R+ Sbjct: 130 RQAQAALDLIGVDV-DLNAEVGSLGIARQQMVEIAKALSMNARILILDEPTAALTGREVD 188 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 + +D+++ +GVA+VFI+H++ +G+ +VL G+ + + +EL +M Sbjct: 189 QLFKVVDELKAKGVAMVFISHHLDEIARIGNTVSVLRDGQFIAELP-ANTDEDELVRLMV 247 Query: 246 G 246 G Sbjct: 248 G 248 Score = 82.8 bits (203), Expect = 1e-20 Identities = 59/229 (25%), Positives = 108/229 (47%), Gaps = 9/229 (3%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 + +PL+ + K+ + + VS+ V GE L G GAG++ +++++GV + G Sbjct: 262 LGKPLLEV----KNLSAAGRFSNVSLTVRAGEVVGLAGLVGAGRTEVVRSIAGVDRVDSG 317 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLM---SVSRNFFMGNEPIRKIGPLKLF 119 +++ G+ L D +AI GI + + L+ SV N +G + L Sbjct: 318 EVIVAGKKLRGGDISEAIKNGIGHIPEDRKAQGLVLGSSVEDN--LGLATLASTAKAGLV 375 Query: 120 DHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSAL 179 D + + +K+ I + Q + LSGG +Q R V G+ VL+LDEPT + Sbjct: 376 DRKGQHERAADVAKKLRIRMANIKQPIKDLSGGNQQKAVFGRWVLAGSNVLLLDEPTRGV 435 Query: 180 GVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLG 228 V + I+++ +G AV+ ++ + L + DR V++ G+ G Sbjct: 436 DVGAKVEIYNIINEITARGGAVLMVSSELPEVLGMADRILVMSGGRIAG 484 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: 343 Number of extensions: 18 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: 523 Length adjustment: 30 Effective length of query: 231 Effective length of database: 493 Effective search space: 113883 Effective search space used: 113883 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 24 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