Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_024980276.1 BXU11_RS09570 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_002017945.1:WP_024980276.1 Length = 228 Score = 130 bits (326), Expect = 3e-35 Identities = 82/202 (40%), Positives = 113/202 (55%), Gaps = 4/202 (1%) Query: 28 HVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVDGVELTN--DLKQI 85 +VLK I+L + +GE + L GPSGSGKST + L L+ G +++G +++ D + Sbjct: 23 YVLKGIDLEINKGEYVALMGPSGSGKSTLMNLLGCLDTPTSGTYILNGKDVSKMKDDELA 82 Query: 86 EAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHK 145 E +E+G VFQ FNL P T L N L PM K + A L +V + ++ Sbjct: 83 EIRNKEIGFVFQTFNLLPRTTALDNVAL-PMIYAGHSKTERTTRATEVLNQVNLGDRMDH 141 Query: 146 YPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMIGLAEDGMTMLCV 205 P QLSGGQ+QRVAIARAL KP I+L DEPT LD + E++ + G T++ V Sbjct: 142 QPNQLSGGQRQRVAIARALVNKPSIILADEPTGNLDSKTSVEIMKLFGDIHAQGNTVILV 201 Query: 206 THEMGFARTVANRVIFMDKGEI 227 THE A A+RVI + G I Sbjct: 202 THEEDIA-AYAHRVIRLRDGLI 222 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: 128 Number of extensions: 6 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: 254 Length of database: 228 Length adjustment: 23 Effective length of query: 231 Effective length of database: 205 Effective search space: 47355 Effective search space used: 47355 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