Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_086508347.1 BZY95_RS02055 ABC transporter
Query= uniprot:Q31RN9 (396 letters) >NCBI__GCF_002151265.1:WP_086508347.1 Length = 233 Score = 84.0 bits (206), Expect = 4e-21 Identities = 67/216 (31%), Positives = 113/216 (52%), Gaps = 22/216 (10%) Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLP---LVTILFFG 246 G +TL A++S++ +L LG+L A + S + ++ Y + RG+P L+ +LFFG Sbjct: 14 GAGVTLQLAVLSLILALILGLLTASAKMSRNWLLHKVATLYTTVIRGVPDLVLMLLLFFG 73 Query: 247 -QVMVPLMLDS-------EWRIDRILRAIVGLTI--FLSAYLAETVRGGLQAIPQGQFEA 296 Q+ + + D+ +W I+ A LTI AY+ ET RG A+ GQ EA Sbjct: 74 GQMALNVATDAIYDRFGVDWYINLNAFAAGVLTIGFIFGAYMGETFRGAFMAVEHGQIEA 133 Query: 297 AAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGI----SRS 352 A G++ + +R I PQ +R ++P I ++ LL+ T L+S++GL +++ + SR+ Sbjct: 134 GKAYGMSPWLVFRRIRFPQMMRHALPGISNNWMVLLKTTALVSVIGLSDMVRVAAEASRA 193 Query: 353 ILANPAYLGRYAEVYLFL-GVLYWLCCYGLAQLSRR 387 +L A VYL + V W+ A+L +R Sbjct: 194 THEPFTFLIPVAVVYLLIASVSEWM----FARLQKR 225 Lambda K H 0.329 0.142 0.471 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: 229 Number of extensions: 12 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: 396 Length of database: 233 Length adjustment: 27 Effective length of query: 369 Effective length of database: 206 Effective search space: 76014 Effective search space used: 76014 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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