Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 148 bits (373), Expect = 3e-40 Identities = 82/242 (33%), Positives = 136/242 (56%), Gaps = 9/242 (3%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 +I M+ I K F ++A V++ V GE H LLG+NGAGKST + + G+++P KG+IL Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIR--KIGPLKLFDHDYA 124 +G+P+ DP A GI VHQH ++ +V+ N +G EP KI K A Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKK------A 117 Query: 125 NRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQT 184 + ++ G+ + P + +S G +Q V I + ++ GA++LI DEPT+AL ++ Sbjct: 118 AKAVETISKQYGLAV-DPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEI 176 Query: 185 ANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMM 244 ++ + K+ +G +++ ITH ++ + V DR TV+ RG+ +GT + + + L MM Sbjct: 177 TELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMM 236 Query: 245 AG 246 G Sbjct: 237 VG 238 Score = 79.7 bits (195), Expect = 1e-19 Identities = 60/239 (25%), Positives = 104/239 (43%), Gaps = 5/239 (2%) Query: 13 IEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLH 72 + K + A+ + ++V GE + G +G G++ I+ ++G+ KPT G+I GQ + Sbjct: 263 VVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDIT 322 Query: 73 FADPRDAIAAGIATV----HQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRIT 128 PR AG+ + H+H ++ +V N + + + + + + Sbjct: 323 GLTPRKITGAGVGHIPQDRHKH-GLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKA 381 Query: 129 MEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVL 188 E + + LSGG +Q IAR V +LI +PT L V ++ Sbjct: 382 NELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIH 441 Query: 189 ATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247 + K R +G AV+ I+ + L V DR V+ GK + + EL +MAGG Sbjct: 442 HRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAGG 500 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: 348 Number of extensions: 21 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: 509 Length adjustment: 29 Effective length of query: 232 Effective length of database: 480 Effective search space: 111360 Effective search space used: 111360 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