Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_086511667.1 BZY95_RS20095 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_002151265.1:WP_086511667.1 Length = 362 Score = 321 bits (823), Expect = 2e-92 Identities = 180/359 (50%), Positives = 225/359 (62%), Gaps = 3/359 (0%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 M L L++I V + ++L L G+ VLLG T AGKT+LMRIMAGL+ PT GRV Sbjct: 1 MSLILENIDHVVNGAVHIEGVNLELAPGSFNVLLGRTLAGKTTLMRIMAGLEPPTRGRVL 60 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLR--GEKNIDARVREIASRL 118 + G+DVT VR RNV+MVYQQFINYP+M V NIASPLKL + I RV E AS L Sbjct: 61 MHGEDVTRTSVRKRNVSMVYQQFINYPAMTVYDNIASPLKLARVSREEIRRRVHETASML 120 Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178 HI+ LDRYPAELSGGQQQR A+ RAL K A L+L DEPLVNLDYKLREE REEL +LF Sbjct: 121 HIEHLLDRYPAELSGGQQQRTAMGRALVKDADLILFDEPLVNLDYKLREEFREELRELFK 180 Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238 A VYATTEP EAL LGG+TAVL EG+LLQYGPT +V+H P + A FS+PP+N+ Sbjct: 181 ARNCIAVYATTEPNEALALGGHTAVLHEGRLLQYGPTEDVYHRPRDVLTAEMFSEPPINV 240 Query: 239 MAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHAR-PGDVSVAGVVELA 297 + A + V L + GVRAS + + R D+ + V++A Sbjct: 241 VPAIVSGTEVTFDRNVHFPLNRDLAGLSPGQYQFGVRASHIGLERRAKDDLELEVKVDIA 300 Query: 298 EISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAPARP 356 EISGS+TF+H LV LTGV+ F + + ++ + Y F +G + P+RP Sbjct: 301 EISGSETFLHVRNELFHLVLHLTGVYEFAVDQPLKVYFPTHKIYAFDRNGDVVHIPSRP 359 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: 356 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: 362 Length adjustment: 29 Effective length of query: 334 Effective length of database: 333 Effective search space: 111222 Effective search space used: 111222 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 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