Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate BPHYT_RS24185 BPHYT_RS24185 C4-dicarboxylate ABC transporter permease
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__BFirm:BPHYT_RS24185 Length = 450 Score = 236 bits (602), Expect = 1e-66 Identities = 143/439 (32%), Positives = 229/439 (52%), Gaps = 22/439 (5%) Query: 1 MALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVP 60 M LA+ S +LLG+P++F L L V ++ + A Q+M+SG + + +AVP Sbjct: 1 MELAILSVSFLVFLLLGVPVSFGLGLACVLTYLY-EGLPAATAMQSMISGINGFSFLAVP 59 Query: 61 FFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALAT 120 FFIL+GELM GGI+ RI+ A + VGH RGGLG + A + +SGS ADT+A+ Sbjct: 60 FFILSGELMLHGGIADRILRFAQATVGHFRGGLGMANVVACTLFGGVSGSPSADTSAMGG 119 Query: 121 LLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIF-----GVT--------TNTSI 167 ++IP+M+ GY + + + ++P S II+ G+T + SI Sbjct: 120 VVIPLMKREGYSAAYAVNVTTHSSLAGALMPTSTNMIIYAFAAQGITGTLNGHPMSGVSI 179 Query: 168 SGLFMAGIVPGL-LMGAGLVIT-WMFVVRGM------TVKLQPKASWGERRTALVEGVWA 219 L +G++P L +MG L+ W V G + +LQ W + + Sbjct: 180 GDLLFSGLLPVLWVMGFVLIAAYWQAVKYGYPRRADGSTELQKFPGWYAVARTFLGALPG 239 Query: 220 LALPVIIIGGLRGGIFTPTEAAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVM 279 L + II+ + GI T TEAA +A YSLV+ + VYR +T+K L L +AA+TT V+ Sbjct: 240 LMVIAIILVCVAKGIATATEAAAIAVFYSLVLTIVVYRSMTMKKLFHALSKAAKTTGVVL 299 Query: 280 FLCAAALVSSYMVTLADLPQQMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVL 339 L + + Y + ++P + ML P L+++ I L+ + +GT +D+ IL+ Sbjct: 300 LLIGVSNMLRYQMAYLEIPDAIEHMLDGATSLPWLMLLYINLIQIFLGTFVDMAAHILIT 359 Query: 340 GPVLTPLAAAAGIDPTYFGVMFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPF 399 P+ P+A AG+ P FG+M +L LGL+HPP+ +V + C + +S+ T+ WP+ Sbjct: 360 TPLFLPMAMHAGVGPVQFGIMILLNCALGLVHPPIGSVQFIGCAIGNVSIGETTKVAWPY 419 Query: 400 LLTYLLLLCLLIAVPEIVT 418 L + ++ VP T Sbjct: 420 YLAIFSAINIVTYVPMFST 438 Lambda K H 0.328 0.142 0.420 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: 412 Number of extensions: 15 Number of successful extensions: 3 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: 426 Length of database: 450 Length adjustment: 32 Effective length of query: 394 Effective length of database: 418 Effective search space: 164692 Effective search space used: 164692 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: 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