Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 164 bits (415), Expect = 4e-45 Identities = 86/222 (38%), Positives = 135/222 (60%), Gaps = 6/222 (2%) Query: 19 IKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPA----- 73 +K +L +N+ E V +G SG GKSTLLR I L + G + ++G DI +V+ Sbjct: 43 VKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQI 102 Query: 74 -KRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILELGPLLERKPK 132 +++LAMVFQ + L PH SV N++F L+L GV K E K E+ +++ L + Sbjct: 103 RRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLVGLKGYENQMVS 162 Query: 133 QLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIYVTH 192 +LSGG +QRV + RA+ NP++ L DE S LD +RVQM+ EL L +++ T++++TH Sbjct: 163 ELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFITH 222 Query: 193 DQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFL 234 D EA+ L D++ ++ G I Q+G+ E+ +PAN +V F+ Sbjct: 223 DLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 264 Lambda K H 0.319 0.136 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: 284 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: 367 Length of database: 408 Length adjustment: 30 Effective length of query: 337 Effective length of database: 378 Effective search space: 127386 Effective search space used: 127386 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: 50 (23.9 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