Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS19725 BPHYT_RS19725 arabinose ABC transporter permease
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS19725 Length = 334 Score = 328 bits (842), Expect = 9e-95 Identities = 160/306 (52%), Positives = 223/306 (72%) Query: 27 AKWWQQITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASR 86 A+ W I + ++++FV++FA +S TV F S N+ GL LS++ IG +S TMMF LA Sbjct: 23 ARTWDLINKSGIVMVFVILFAALSFTVPDFLSSRNIQGLLLSVTLIGSISVTMMFVLALG 82 Query: 87 DFDLSVGSTVAFAGVLCAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITT 146 + DLSV S VAFAGV+ + ++ AT + + + A V AGG +G VNG ++A +IN+LI T Sbjct: 83 EVDLSVASIVAFAGVVASTLITATHSVILGVAAGVLAGGAVGLVNGVLVARYKINSLIVT 142 Query: 147 LATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTV 206 LA ME+VRGL +I S+G AV +S + F LGG +F G+S PIW ++ F++FG +L +TV Sbjct: 143 LAMMEVVRGLAYITSNGDAVMISEERFFDLGGGAFLGISYPIWSNIIGFVLFGFLLKKTV 202 Query: 207 YGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFE 266 +G+N LA+GGN EA+ LAG+ V R ++ +F++QG VT AGV+LASR++ G P + G E Sbjct: 203 FGKNVLAVGGNSEAALLAGLPVTRIKITVFVLQGLVTGFAGVMLASRMSLGDPKTSVGLE 262 Query: 267 LNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAV 326 L VISACVLGGVSL GG ATISGV++GVLIMG+V++ M+L+N+ FYQYL+RG ILL AV Sbjct: 263 LGVISACVLGGVSLTGGVATISGVLVGVLIMGSVQDAMSLLNVPTFYQYLIRGGILLLAV 322 Query: 327 LLDQLK 332 L DQ + Sbjct: 323 LFDQFR 328 Lambda K H 0.326 0.139 0.396 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: 387 Number of extensions: 20 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: 338 Length of database: 334 Length adjustment: 28 Effective length of query: 310 Effective length of database: 306 Effective search space: 94860 Effective search space used: 94860 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: 49 (23.5 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