Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 350388 BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Btheta:350388 Length = 224 Score = 125 bits (315), Expect = 8e-34 Identities = 76/215 (35%), Positives = 121/215 (56%), Gaps = 12/215 (5%) Query: 8 NIRKAYDENEV----MRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTID 63 N++K + EV + ++++++ GEFV +GPSGCGKSTL+ ++ L++ +GG+ ++ Sbjct: 6 NLQKIFKTEEVETWALNNVSIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGGEYYLN 65 Query: 64 GMRVNDVAPAKRG------IAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNA 117 G V+ ++R I VFQS+ L + +Y+N+ L G E V A Sbjct: 66 GTEVSKYTESQRTSLRKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKKRVETA 125 Query: 118 AKILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFA 177 + + I H P+QLSGGQ+QRVAI RA+ PK+ L DEP NLD+ ++ + Sbjct: 126 MERMAITHRSKHFPQQLSGGQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEVMGLLS 185 Query: 178 RLHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNL 212 L+ E TT++ VTH Q +A AD+I+ L G + Sbjct: 186 ELNKE-GTTIVMVTHSQHDA-GYADRIINLFDGQV 218 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: 178 Number of extensions: 8 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: 369 Length of database: 224 Length adjustment: 26 Effective length of query: 343 Effective length of database: 198 Effective search space: 67914 Effective search space used: 67914 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: 47 (22.7 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