Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_002115805.1:WP_085638891.1 Length = 362 Score = 350 bits (898), Expect = e-101 Identities = 195/364 (53%), Positives = 243/364 (66%), Gaps = 5/364 (1%) Query: 1 MASVTLRNIRKAY-DENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MA++ L N+ K Y V+ +INLDI GE +VFVGPSGCGKSTL+RMIAGLE I+GG Sbjct: 1 MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 L IDG VND+ PA RGIAMVFQSYALYPHMT+ +NM+F LK+A + EIDAAV AAK Sbjct: 61 LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 +L +D LDR PK LSGGQRQRVAIGR+I R PKV+LFDEPLSNLDAALRV R+E A+L Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 HDEL-KTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 +++ ++TMIYVTHDQVEAMTLA +IVVL+ + QVG+P LY P + FVA FIGSP Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240 Query: 239 MNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGI- 297 MN + G + T TV+ + G G KV VG+RPE VG + D I Sbjct: 241 MNLLPGEIVG-TGQQTTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDF-VGTSGDHIF 298 Query: 298 SARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDSAGK 357 R E+LG+ LY E +I ++P + +G+T KLGA+P+ H+F + Sbjct: 299 EGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIFHNGTS 358 Query: 358 AFQR 361 R Sbjct: 359 LLYR 362 Lambda K H 0.320 0.135 0.384 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: 400 Number of extensions: 22 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: 369 Length of database: 362 Length adjustment: 30 Effective length of query: 339 Effective length of database: 332 Effective search space: 112548 Effective search space used: 112548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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