Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >MicrobesOnline__882:208681 Length = 349 Score = 174 bits (440), Expect = 4e-48 Identities = 116/349 (33%), Positives = 178/349 (51%), Gaps = 18/349 (5%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 + LD +S+ G + D+S ++ G + VLLG + GK++ +R++AGL++ T+GR+ + Sbjct: 4 IVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRILIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG------EKNIDARVREIAS 116 G+DVT +P R +AMV+Q + +P + V NI L +R +K +D V EI Sbjct: 64 GRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAV-EI-- 120 Query: 117 RLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQL 176 L + L+R P ELSGGQQQRVAL RAL A + L+DEPL NLD KLR+E+R E+ L Sbjct: 121 -LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRAL 179 Query: 177 FAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPM 236 T+VY T + EA+ + ++ G+++Q E++ P + PPM Sbjct: 180 QQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPM 239 Query: 237 NLMAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVEL 296 NL+ G+R+ G + G A +G+R H R D VVE Sbjct: 240 NLVRLQGNDDGIRVAGSRSGRVTCHAG----ADCMLGIRPE----HIRIVDDGWRAVVES 291 Query: 297 AEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGA 345 E GS++ + +L + GV +G I LH ++F A Sbjct: 292 VEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDA 340 Lambda K H 0.318 0.133 0.375 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: 275 Number of extensions: 11 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: 363 Length of database: 349 Length adjustment: 29 Effective length of query: 334 Effective length of database: 320 Effective search space: 106880 Effective search space used: 106880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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