Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_038206815.1 Q392_RS11640 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000745855.1:WP_038206815.1 Length = 394 Score = 557 bits (1436), Expect = e-163 Identities = 277/347 (79%), Positives = 315/347 (90%) Query: 8 WIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 +++ A ALLVLPL+LQ+ GNAWVRI D+ALLYVLLALGLNIVVGYAGLLDLGYVAF+A+G Sbjct: 9 FLVAAAALLVLPLLLQTQGNAWVRIVDIALLYVLLALGLNIVVGYAGLLDLGYVAFFAIG 68 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127 AYLFAL+ S L DNF A AMFPNG HTSL +VIP A ++AA GA+LGAPTLKLRGDY Sbjct: 69 AYLFALLGSTQLTDNFEALKAMFPNGFHTSLILVIPAALVVAALLGALLGAPTLKLRGDY 128 Query: 128 LAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVT 187 LAIVTLGFGEIIR+FLN LDHP N+TNGPKG+ IDS+++FGL+LG+ L++ + I+SV+ Sbjct: 129 LAIVTLGFGEIIRVFLNTLDHPYNVTNGPKGITGIDSIRIFGLNLGRPLKIGDYTISSVS 188 Query: 188 LYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASF 247 LYYYLFLVLV+ +VII YRLQ SR+GR WMAIREDEIAAKAMGINTRNMKLLAFGMGASF Sbjct: 189 LYYYLFLVLVIFTVIISYRLQSSRVGRGWMAIREDEIAAKAMGINTRNMKLLAFGMGASF 248 Query: 248 GGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYV 307 GGVSGAMF AFQGFVSPESF+LMESVMIV+MVVLGGIGH+PGVILGAVLL+ALPEVLRYV Sbjct: 249 GGVSGAMFAAFQGFVSPESFNLMESVMIVSMVVLGGIGHLPGVILGAVLLAALPEVLRYV 308 Query: 308 AGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSL 354 AGPLQ+MTDGRLD++ILRQL IAL+MI+IML RPRGLWPSPEHGKSL Sbjct: 309 AGPLQSMTDGRLDASILRQLFIALSMILIMLTRPRGLWPSPEHGKSL 355 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: 469 Number of extensions: 11 Number of successful extensions: 1 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: 394 Length adjustment: 30 Effective length of query: 328 Effective length of database: 364 Effective search space: 119392 Effective search space used: 119392 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