Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00010 (365 letters) >FitnessBrowser__ANA3:7023042 Length = 367 Score = 140 bits (352), Expect = 7e-38 Identities = 89/222 (40%), Positives = 127/222 (57%), Gaps = 14/222 (6%) Query: 23 DLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSG------TIELDGRDITEVTPAKRD 76 + K E + VGPSG GK+TLLR+IAGL +G T+ D + T +TP +R Sbjct: 23 EFSCKAGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTALTPQQRH 82 Query: 77 LAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILE---LGSLLDRKPKQ 133 + + Q + L+P++T +N+ LD P ER +A A LE L L DR P Sbjct: 83 IGYMPQHFGLFPNLTALENVVAGLDHI----PKSER-IARAKDWLERVNLHGLPDRLPMH 137 Query: 134 LSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKELQATMIYVTHD 193 LSGGQRQRVA+ RA+ R P + L DEP S +D R + LEL+RL ++L +I VTHD Sbjct: 138 LSGGQRQRVALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIMVTHD 197 Query: 194 QVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLG 235 EA+ LA +++++ G++ Q G+P E+ P N VA +G Sbjct: 198 LNEALLLADSMILISQGQMLQQGAPFEVLSRPRNEAVARQMG 239 Lambda K H 0.319 0.136 0.381 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: 250 Number of extensions: 14 Number of successful extensions: 3 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: 365 Length of database: 367 Length adjustment: 30 Effective length of query: 335 Effective length of database: 337 Effective search space: 112895 Effective search space used: 112895 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