Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012116023.1 XAUT_RS20495 ABC transporter
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000017645.1:WP_012116023.1 Length = 663 Score = 165 bits (417), Expect = 4e-45 Identities = 98/311 (31%), Positives = 169/311 (54%), Gaps = 29/311 (9%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68 I+G AL VLP ++ S ++ + +Y +L LGL++V GY G + +G+ A + +GA Sbjct: 13 ILGLAALAVLPFVVTS--PYYLHLTITIAIYAILLLGLDVVFGYTGEVSIGHAALFGIGA 70 Query: 69 YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128 Y +A H F W +P+A ++ A FG +L P L++ G YL Sbjct: 71 YTAGCLAM-HFGIGF---------------WPALPLAIIVTALFGIVLALPALRVTGPYL 114 Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSV-- 186 A+VTL FG I++I +N + +LTNGP G+ + + LG + +F + + Sbjct: 115 AMVTLAFGTIVQILINEM---TDLTNGPLGIKLTTPLFLDLRWLGDTIPLFDMSLKRMKE 171 Query: 187 TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGAS 246 Y+Y+ V +V+++++ R+ S +GRA+ A+R+ IA+ MG++ K++AF + A Sbjct: 172 VEYFYIAAVALVLTLLVINRILASHLGRAFEALRDSPIASDCMGVSVYKHKVIAFVVSAG 231 Query: 247 FGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVL-- 304 F G++GA+F + +++P +F SV + V +GG G I+GAV++ LP +L Sbjct: 232 FAGLAGALFAYSEQYIAPNNFGFELSVQFLLAVTVGGRKSRLGPIIGAVIIVFLPNLLSD 291 Query: 305 ----RYVAGPL 311 RY+AG + Sbjct: 292 IVLFRYIAGTI 302 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: 477 Number of extensions: 23 Number of successful extensions: 4 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: 663 Length adjustment: 34 Effective length of query: 324 Effective length of database: 629 Effective search space: 203796 Effective search space used: 203796 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: 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