Align ABC transporter related (characterized, see rationale)
to candidate WP_040912583.1 ON01_RS16055 sugar ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >NCBI__GCF_000224785.1:WP_040912583.1 Length = 491 Score = 352 bits (904), Expect = e-101 Identities = 182/496 (36%), Positives = 311/496 (62%), Gaps = 9/496 (1%) Query: 7 LKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGE 66 ++ ISK + G + L+ V+ + GEVHAL+GENGAGKSTL+K++TG +D G + G+ Sbjct: 1 MQGISKSFSGNQVLKSVNFSVDKGEVHALVGENGAGKSTLIKILTGIHKRDEGAVRINGK 60 Query: 67 PQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR--RLGLIHFKKMYADARAV 124 HF+ P +A++ GI ++QE+N++P+LTV +N+FLG + G+++ K+M +A Sbjct: 61 EVHFSHPKEAEQQGIMVIHQELNIIPHLTVTENMFLGKNIAYGKTGILNTKEMRKQCKAN 120 Query: 125 LTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 L + + ID D S+ QQ+I IAR V+ +A+++V+DEPTA+L +E+ LF ++ Sbjct: 121 LERLGVSTIDPDDIAGDLSVGKQQMIEIARAVSTNAELIVMDEPTAALTDREIDSLFEVI 180 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 L+ GVA+++I+H ++++++I DRITVLR+G++IG ++ +++ M+GR L E Sbjct: 181 QSLRKNGVAVIYISHRMEEIFRICDRITVLRDGEYIGTKNVTDVDFDGIVKMMVGRELGE 240 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 + ER T + V+ ++ ++ KG ++ +V +G+ +G+AGL+G+GRSE+ Sbjct: 241 RF-----PERDYTGGD-VIFEVKSLARKGLFDDISFSVKEGEILGVAGLMGAGRSEIMET 294 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363 +FG +GSIHL G++L + P DAI AGI EDRK G++ SI +NI L Sbjct: 295 IFGYTHKQNGSIHLNGKELPIKHPSDAIKAGIGFITEDRKSKGLLTDFSIGDNISLTNMK 354 Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423 + +S ++ + +D+L++ A + + LSGGNQQKV++A+WL IEP LL+ Sbjct: 355 SVSSNGIISANKEHRLIAELMDRLKVKATGATQEAKALSGGNQQKVVIAKWLGIEPKLLI 414 Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483 LDEPTRG+D+GA EI ++ L G+++++ SS+L E++ S++++V+ + Sbjct: 415 LDEPTRGVDVGAKKEIYNIMNELTKNGVAIIMVSSDLPEVLGVSDRIMVIYEGRIANIFD 474 Query: 484 GAELTSQHVMQAIAEG 499 + +++M A A G Sbjct: 475 RDQADQENIMTAAAGG 490 Lambda K H 0.319 0.136 0.377 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: 556 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 491 Length adjustment: 34 Effective length of query: 465 Effective length of database: 457 Effective search space: 212505 Effective search space used: 212505 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 (21.8 bits) S2: 52 (24.6 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