Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 372 bits (954), Expect = e-107 Identities = 198/369 (53%), Positives = 249/369 (67%), Gaps = 2/369 (0%) Query: 1 MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 MASVTL I K + +++D++L I +GEFVVFVGPSGCGKSTL+R+IAGLE I+ G+L Sbjct: 1 MASVTLDKINKVFGSTHIIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLESITDGEL 60 Query: 61 TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120 +I VN++ P +RG+ MVFQSYALYPHMT+Y+NMAFGLKLA T K + V A+I Sbjct: 61 SIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERVMATARI 120 Query: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180 L ++ LL+RKPK LSGGQRQRVA+GRA+ R+P++ LFDEPLSNLDA+LRV+MR E ARLH Sbjct: 121 LQLEELLERKPKALSGGQRQRVAMGRAMAREPRILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240 L +TM+YVTHDQVEAMTLADKIVVL G +EQVGSP LY PA +FVAGFIGSP MN Sbjct: 181 KRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGFIGSPTMN 240 Query: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPAA-VKQGDKVTVGIRPEHLHVGMAEDGISA 299 F+ + G + TG T+ + A+ QG +T+GIRPEHL + A+ Sbjct: 241 FLPARLLGADATGCRIG-ATGLTELALPQDASGHAQGAALTLGIRPEHLRLSEAQGSEGF 299 Query: 300 RTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDSAGKAF 359 + VE LG+ Y+Y E LI R G+ L PEH HLFD+ G+A Sbjct: 300 EIVNVEYLGNEVYVYLEPKEGETLLIQRGEAPTTWRVGQRVTLAPDPEHVHLFDAGGRAL 359 Query: 360 QRKIVEVLA 368 K +A Sbjct: 360 SVKAARAVA 368 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: 430 Number of extensions: 22 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: 368 Length adjustment: 30 Effective length of query: 339 Effective length of database: 338 Effective search space: 114582 Effective search space used: 114582 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