Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 159 bits (402), Expect = 1e-43 Identities = 86/250 (34%), Positives = 147/250 (58%), Gaps = 8/250 (3%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 PL+ ++G+ K FG V+A +S++++PG LLG+NGAGKST + ++G ++P G I Sbjct: 23 PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +G+P+ F+ RDAI AGI V+QH ++ M+V+ N +G E G L + N Sbjct: 83 LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE-----GSFFLNPKEMRN 137 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 R+ E + G+++ P V LS GE+Q V I + ++ ++VLI DEPT+ L R+T Sbjct: 138 RV-QELSVRYGLDI-DPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE-ELQDMM 244 ++ + K+ +QG ++VFI+H + LAV D +L +G+ G +++++ +L M Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255 Query: 245 AGGQELATLE 254 G + L ++ Sbjct: 256 VGKEVLLEVD 265 Score = 55.8 bits (133), Expect = 2e-12 Identities = 57/240 (23%), Positives = 103/240 (42%), Gaps = 21/240 (8%) Query: 21 IALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH--FADP-- 76 I L ++ D+ GE ++G G G+ ++ + G+ KP + G+ +A P Sbjct: 284 IGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSW 343 Query: 77 RDAIA------AGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITME 130 ++++A G+AT + L+ +R F GP D A R T E Sbjct: 344 KNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFAR-------GPW--LDKKKAARDTTE 394 Query: 131 EMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLAT 190 ++K I LSGG Q +AR ++ ++++ ++PT L + T V Sbjct: 395 LIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNH 454 Query: 191 IDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGD-ISAEELQDMMAGGQE 249 + R+ ++ +T ++ AL + DR V+ RG+ + D + MMAG +E Sbjct: 455 LLAAREM-AGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVEE 513 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: 299 Number of extensions: 13 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: 514 Length adjustment: 29 Effective length of query: 232 Effective length of database: 485 Effective search space: 112520 Effective search space used: 112520 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 Apr 09 2024. 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