Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 157 bits (398), Expect = 6e-43 Identities = 94/301 (31%), Positives = 164/301 (54%), Gaps = 41/301 (13%) Query: 9 IIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 + A+AL+ L + GN + + + + ++Y +L GL+IVVGY G + LG+ + VG Sbjct: 7 VASALALIALAVFPVLSGNPYYIHLLETIMIYAILLFGLDIVVGYTGQVSLGHAGLFGVG 66 Query: 68 AY----LFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123 AY LF + P + + P+A L+ A FGA+L P L++ Sbjct: 67 AYTAGVLFFKLGMPFI--------------------VTAPLAILITAAFGAILALPALRV 106 Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI 183 G YLA+VTL FG I++I +N +D LTNGP G VK+ + + G + Sbjct: 107 SGPYLAMVTLAFGTILQILINEMDF---LTNGPMG------VKI------PKPSLAGRPM 151 Query: 184 NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGM 243 N V YY+L L+V S+I+ +R+ S +GRA+ A+R+ IA+ MG++ K+ AF + Sbjct: 152 NEVE-YYWLVAALLVASLIVVHRVLRSHLGRAFEALRDSPIASDCMGVSVYRYKVYAFVI 210 Query: 244 GASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEV 303 A F G++G ++ + ++SP +++ +++ + +++GG G +LG+ ++ LP++ Sbjct: 211 SAGFAGLAGCLYSYSEQYISPNTYNFELTILFLLAIIMGGRKTRTGALLGSAIIVLLPKL 270 Query: 304 L 304 L Sbjct: 271 L 271 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: 444 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 646 Length adjustment: 34 Effective length of query: 324 Effective length of database: 612 Effective search space: 198288 Effective search space used: 198288 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: 51 (24.3 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