Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 140 bits (354), Expect = 4e-38 Identities = 87/235 (37%), Positives = 137/235 (58%), Gaps = 7/235 (2%) Query: 3 LALDSISKKVGAQTW-LYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61 L + +SK+ A + L D SL ++ G V ++G + +GK+SL+RI+AGL+ +AG V + Sbjct: 4 LKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHL 63 Query: 62 DGKDVTG-----MPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIAS 116 + + +P D + +++Q++ YP+ V NIA PL L + R EI Sbjct: 64 GDQKILNPAQKLVPGYDE-IQLIHQEYKLYPNSTVEENIARPLLLYDKAYQKERTAEILE 122 Query: 117 RLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQL 176 L + F D+ P +LSGGQQQ+VA+ RAL+ ++LLDEP +LD + +L EEL ++ Sbjct: 123 LLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEI 182 Query: 177 FAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAF 231 F A + TV++ T + +ALL+ ++ +G+LLQ G EVF P S VAR F Sbjct: 183 FDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237 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: 218 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: 363 Length of database: 318 Length adjustment: 28 Effective length of query: 335 Effective length of database: 290 Effective search space: 97150 Effective search space used: 97150 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