Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_086508440.1 BZY95_RS02565 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_002151265.1:WP_086508440.1 Length = 240 Score = 268 bits (685), Expect = 8e-77 Identities = 131/240 (54%), Positives = 177/240 (73%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I + ++K++G+ HVLK ++L V+ E +VL G SGSGKST +RCLN LE +G IV+ Sbjct: 1 MITVSNLHKYFGELHVLKGVDLEVRPREVVVLIGASGSGKSTLLRCLNFLELKDEGSIVI 60 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DG E+ + +R VGMVFQHFNLFPH+T+L+N AP+ V+++PK +A E A Sbjct: 61 DGQEIDPATTPLNKVRENVGMVFQHFNLFPHMTVLENVIEAPVHVKRIPKAEAIERARQL 120 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L++V + +++ YP +LSGGQ+QRVAIARAL M+P +MLFDEPTSALDPE+V EVL+ M Sbjct: 121 LDKVGLGDKSDAYPEKLSGGQKQRVAIARALAMEPSVMLFDEPTSALDPELVGEVLEVMK 180 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 GLA DGMTM+ VTHEMGFAR VA+RV+F+D G I EQ P F NPQ+ + + FLS++L Sbjct: 181 GLAADGMTMVVVTHEMGFAREVADRVVFLDGGTIAEQGPPGTLFSNPQHPKARQFLSRVL 240 Lambda K H 0.322 0.137 0.407 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: 205 Number of extensions: 11 Number of successful extensions: 1 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: 254 Length of database: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 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 (21.9 bits) S2: 46 (22.3 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