Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate HSERO_RS15485 HSERO_RS15485 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__HerbieS:HSERO_RS15485 Length = 349 Score = 194 bits (492), Expect = 4e-54 Identities = 116/343 (33%), Positives = 185/343 (53%), Gaps = 8/343 (2%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 ++L + K G + ++ +++G TVLLG + GK++ +R++AGLD P++G + + Sbjct: 4 ISLQGVCKHWGEAQAVRNIDFEVKAGQFTVLLGPSGCGKSTTLRLIAGLDKPSSGSIHIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNI--DARVREIASRLHI 120 G+DVT +P R ++MV+Q + +P + V NI +++R E + R++ +A L + Sbjct: 64 GRDVTQLPPAQRKISMVFQSYALFPHLSVRDNILFGVRVRKEPRAGYETRLKRVADILGL 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 L+R PA+LSGGQQQRVAL RA+ AP+ L+DEPL NLD +LR+E+R E+ L Sbjct: 124 AHLLERRPAQLSGGQQQRVALGRAIIADAPVCLMDEPLSNLDAQLRQEMRREIRALQQQL 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 T+VY T + EA+ + +L EG++ Q A+++ P + AR PPMNL+ Sbjct: 184 NMTMVYVTHDQTEAMSMADQVILLREGRIEQDAAPADLYAQPATAFAARFIGTPPMNLLP 243 Query: 241 ASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300 A+G+ + G + L Q +G+R +R+ A D SV VVE E Sbjct: 244 LEPHAEGLVISGSDVILRDLGQ-----TPWQLGLRPEHIRL-ADASDSSVPAVVETVEYF 297 Query: 301 GSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVF 343 G+DT + A L+ + G H G + L D Y F Sbjct: 298 GADTIIGARIGAASLLVRAPGQHRLGAGDPVRLAWDARDQYFF 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: 299 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: 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