Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084544685.1 H566_RS22525 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000482785.1:WP_084544685.1 Length = 403 Score = 478 bits (1230), Expect = e-139 Identities = 234/348 (67%), Positives = 282/348 (81%), Gaps = 2/348 (0%) Query: 6 TNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYA 65 T ++ A L VLP + SFGNAWVRI D ALLYV+LALGLNIVVG+AGLLDLGY+AFYA Sbjct: 35 TAMLVTAAILAVLPFAVGSFGNAWVRILDFALLYVMLALGLNIVVGFAGLLDLGYIAFYA 94 Query: 66 VGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRG 125 VGAY++ L+ASPHL D F A AA+ P+G+H +W VIP+A LAA FG +LGAPTLKLRG Sbjct: 95 VGAYMYGLLASPHLTDTFPAIAALVPDGMHVPVWFVIPLAGGLAALFGVLLGAPTLKLRG 154 Query: 126 DYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINS 185 DYLAIVTLGFGEIIRIF+ NL+ P+N+TNGP+G+ ID + LGKR E+FG Sbjct: 155 DYLAIVTLGFGEIIRIFMLNLNQPLNITNGPQGINLIDPIAFGDFSLGKRHELFGTKYAG 214 Query: 186 VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGA 245 YYY+FL L V+++I C RLQDSRIGRAWMAIREDEIAAKAMGINTRN+KLLAF MGA Sbjct: 215 TYFYYYVFLGLTVLTIIACNRLQDSRIGRAWMAIREDEIAAKAMGINTRNIKLLAFAMGA 274 Query: 246 SFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLR 305 SFGGV+G+MF AFQGF+SPESFSLMES++++AMVVLGG+GHIPGV+ GAVLL+ PE LR Sbjct: 275 SFGGVAGSMFAAFQGFISPESFSLMESIVVLAMVVLGGMGHIPGVVFGAVLLAVFPEALR 334 Query: 306 YVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEHG 351 YVAGP+Q G +D+ +LR L+ +AM+ IMLLRP+GLWP+P+HG Sbjct: 335 YVAGPVQEAIFGSVLVDAEVLRMLIYGVAMVAIMLLRPKGLWPAPQHG 382 Lambda K H 0.328 0.144 0.430 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: 502 Number of extensions: 15 Number of successful extensions: 2 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: 358 Length of database: 403 Length adjustment: 30 Effective length of query: 328 Effective length of database: 373 Effective search space: 122344 Effective search space used: 122344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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