Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate GFF5095 PS417_26105 ABC transporter permease
Query= uniprot:Q88GX3 (239 letters) >FitnessBrowser__WCS417:GFF5095 Length = 239 Score = 366 bits (939), Expect = e-106 Identities = 188/238 (78%), Positives = 211/238 (88%) Query: 1 MLDQLSLLSFASGGWGQALLAGALVTVSLALACLPIGLPLGLVVALAARSRKRLPRAWAT 60 ML+QLSLLSFA+GGWG ALLAGALVT++LALAC+P+GLPLGL+VALAARS++R R AT Sbjct: 1 MLEQLSLLSFANGGWGSALLAGALVTITLALACIPLGLPLGLLVALAARSKRRWLRTGAT 60 Query: 61 TFSTVFRGLPELLTLLIIYYGCQIAAQKILAAMGYQGEFLINTFLAAMIAFSLVFAAFSS 120 FSTVFRGLPELLTLLIIYYGCQIAAQ++LAAMGYQGE INTF+AAMIAFSLVFAAFSS Sbjct: 61 VFSTVFRGLPELLTLLIIYYGCQIAAQRMLAAMGYQGEVTINTFVAAMIAFSLVFAAFSS 120 Query: 121 EIWLAAFKTLPKGQLEACSALGLSKRTGFFKVLLPQLTRIALPGLSNNWLSLLKDTSLVS 180 E+WL+AFK+L KGQ EA + LGL K T KV+LPQLTRIALPGLSNNWLSLLKDTSLVS Sbjct: 121 EVWLSAFKSLSKGQFEAATMLGLPKGTTLRKVVLPQLTRIALPGLSNNWLSLLKDTSLVS 180 Query: 181 TISLVDLMRQTNLAVSVTKEPMFFYGVACLGYLLFAALSGRVFAYIERRSNRHLQGAR 238 TISLVDLMRQT+LAVSVTKEPM FY VAC GYL F+ALSGRVF ++ER +RH A+ Sbjct: 181 TISLVDLMRQTSLAVSVTKEPMLFYAVACFGYLFFSALSGRVFNFLERYFSRHQLSAK 238 Lambda K H 0.328 0.139 0.410 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: 266 Number of extensions: 12 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: 239 Length of database: 239 Length adjustment: 23 Effective length of query: 216 Effective length of database: 216 Effective search space: 46656 Effective search space used: 46656 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 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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