Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 117 bits (294), Expect = 3e-31 Identities = 78/237 (32%), Positives = 123/237 (51%), Gaps = 15/237 (6%) Query: 7 DLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVL 66 +L+HSYK + L + + G A++G SGCGK+T+L +++GLL+PS G V Sbjct: 12 ELSHSYK----KQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVR 67 Query: 67 FDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEML 126 +G+ V + S + +FQ P +Y M+V EN A L V G KQ+ + E+L Sbjct: 68 INGKTVVKPSAKWN---MMFQKPSLYPWMSVRENAALGL----VFAGTYKQKQDRVEELL 120 Query: 127 EMSG---QLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLK 183 +M G ++ L+ +Q+++L R L + +L DEP + +D + L+ ++ Sbjct: 121 DMVGLSEHKDKNVQELSGGQQQRVALARSLA-TEPEILLLDEPFSALDAFTRTALQTEVA 179 Query: 184 QIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFI 240 QI HE +T+I VTHD EA+ AD+VV+M+ VG D P FI Sbjct: 180 QICHEQGITMIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236 Lambda K H 0.320 0.136 0.395 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: 200 Number of extensions: 10 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: 358 Length of database: 263 Length adjustment: 27 Effective length of query: 331 Effective length of database: 236 Effective search space: 78116 Effective search space used: 78116 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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