Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 363 bits (931), Expect = e-105 Identities = 203/364 (55%), Positives = 245/364 (67%), Gaps = 4/364 (1%) Query: 1 MASVTLRNIRKAYDEN-EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MA++ L N+ K Y EV+RDINLDI GE +VFVGPSGCGKSTL+RMIAGLE ISGG Sbjct: 1 MANLKLTNVAKTYGGGVEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGGT 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 L ID +ND+ PA+RGIAMVFQSYALYPHMT+ DNMAF LK+A K EIDAA+ AAK Sbjct: 61 LEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAAK 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 IL ++ LDR PK LSGGQRQRVAIGR+I R PKV+LFDEPLSNLDAALRV R+E A+L Sbjct: 121 ILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 HDEL-KTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 + + +TMIYVTHDQVEAMTLA +IVVL+ + QVG+P LY P N FVA FIGSP Sbjct: 181 KEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSPA 240 Query: 239 MNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHL-HVGMAEDGI 297 MN + G V + T TVR +GE + QG V VG+RPE L G I Sbjct: 241 MNLIPGTVVA-TGPRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEEGTGGALI 299 Query: 298 SARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDSAGK 357 +R VE+LG+ LY + D LIA++P + + +G + +L A P HLF + Sbjct: 300 DSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHLFHNGQS 359 Query: 358 AFQR 361 R Sbjct: 360 LLYR 363 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: 15 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: 369 Length of database: 363 Length adjustment: 30 Effective length of query: 339 Effective length of database: 333 Effective search space: 112887 Effective search space used: 112887 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 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