Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate RR42_RS13790 RR42_RS13790 ABC transporter
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Cup4G11:RR42_RS13790 Length = 366 Score = 484 bits (1245), Expect = e-141 Identities = 254/357 (71%), Positives = 288/357 (80%), Gaps = 2/357 (0%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 MQL L+ I+++ G+Q +LY MSL GAVT+LLGATQAGKTSLMR+MAGLD P+AGRV Sbjct: 1 MQLRLEGIAQQAGSQAYLYPMSLTPVPGAVTILLGATQAGKTSLMRVMAGLDRPSAGRVE 60 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHI 120 VDG DVTGMPVR+RNV+MVYQQFINYPSM V NIASPLKLR ++ID +VR +A+RLHI Sbjct: 61 VDGIDVTGMPVRERNVSMVYQQFINYPSMTVFDNIASPLKLRRSRDIDGQVRALATRLHI 120 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 + L+R+PAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA G Sbjct: 121 EHLLERFPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAHG 180 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 +TV+YATTEP EALLLGGYTAVLD G+LLQYGPT EVFH P SLRVARAFSDPPMNLMA Sbjct: 181 NATVIYATTEPAEALLLGGYTAVLDAGELLQYGPTPEVFHYPASLRVARAFSDPPMNLMA 240 Query: 241 ASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300 + A V L GG + +PLP +TVGVRA ALR+ A PG V VAG V LAE+S Sbjct: 241 GNLLAGAVTLPGG--VVVPLPGAVEQGGTVTVGVRAGALRLDAVPGSVPVAGRVALAELS 298 Query: 301 GSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAPARPV 357 GSDTFVH +P G+LVAQ GV ELG +TLHLDPAQ Y+F ADG AP+RP+ Sbjct: 299 GSDTFVHMDSPVGNLVAQFPGVVDLELGAPLTLHLDPAQLYLFDADGMRIHAPSRPL 355 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: 477 Number of extensions: 14 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: 363 Length of database: 366 Length adjustment: 29 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 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