Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate BPHYT_RS33295 BPHYT_RS33295 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS33295 Length = 362 Score = 408 bits (1048), Expect = e-118 Identities = 211/360 (58%), Positives = 265/360 (73%), Gaps = 7/360 (1%) Query: 1 MARISL-DLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLV 59 MARI +LAH+Y PNP DYAL P+ M +EDGGAYALLGPSGCGK+T+LNI+SGL+ Sbjct: 1 MARIEFQNLAHAYAPNPATLDDYALQPMSMVWEDGGAYALLGPSGCGKSTLLNIVSGLVT 60 Query: 60 PSHGKVLFDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRV 119 PS GKVLFDG D+T SP+ERNIAQVFQFPVIYDTM+V +NLAFPLRNRK+ +KQRV Sbjct: 61 PSEGKVLFDGSDITAKSPRERNIAQVFQFPVIYDTMSVFDNLAFPLRNRKMSAHDVKQRV 120 Query: 120 GVIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLR 179 +AE+L+M+ +L ++A L+ADAKQKISLGRGLVR DVAA+LFDEPLTVIDPH+KW LR Sbjct: 121 HEVAEILDMTRELPRKANNLSADAKQKISLGRGLVRKDVAAILFDEPLTVIDPHMKWILR 180 Query: 180 RKLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHF 239 R+LK+IH +LKLTLIYVTHDQVEALTFAD+VVVMT G+ VQ G ALF RP H FVG+F Sbjct: 181 RQLKKIHQQLKLTLIYVTHDQVEALTFADEVVVMTNGRVVQKGDPGALFLRPDHAFVGYF 240 Query: 240 IGSPGMNFLP--AHRDGENLSVAGHRLASPVGRAL--PAGALQVGIRPEYLALAQPQQAG 295 IGSPGMN P + DG + +L P L G L +GIRPE++ +A +AG Sbjct: 241 IGSPGMNLCPIELNADGIKIGTQHLQLDPPTLETLRHANGTLTLGIRPEFVRVASDGEAG 300 Query: 296 ALPGTVVQVQDIGTYQMLTAKVGEHTVKARFTPETRLPSSGDTAWLQVLGEHTCYYKNEE 355 A+ +++VQ +G YQ++TA+ H +A+ P R+ WL++ T ++ N+E Sbjct: 301 AVKAHLLRVQQLGNYQLVTAQCDGHVFRAKVEPHLRVGEG--AVWLKLATAETVFFSNDE 358 Lambda K H 0.320 0.136 0.395 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: 386 Number of extensions: 15 Number of successful extensions: 2 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: 358 Length of database: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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