Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >NCBI__GCF_003173355.1:WP_109969962.1 Length = 225 Score = 95.5 bits (236), Expect = 1e-24 Identities = 67/214 (31%), Positives = 117/214 (54%), Gaps = 16/214 (7%) Query: 187 DW-----SGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVT 241 DW SG+ +T+ ++++ + LG+ +ALG+ IR + Y+ FRGLP++ Sbjct: 9 DWFPYLLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLV 68 Query: 242 ILF---FGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAA 298 +LF FG + L LD + + V L + +AY ++ RG +Q+I +GQ AA Sbjct: 69 LLFLFYFG-IFPGLGLD----LPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMTAAR 123 Query: 299 ALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPA 358 +LG++ Q R I+LPQA+RI++P + +L ++++ +G+ ELL S I++ Sbjct: 124 SLGMSRAQAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQIVSQ-T 182 Query: 359 YLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 Y+ +YL V++ L Y L +RLE+R+ Sbjct: 183 YV--TMPIYLACAVMFILLSYAGTHLIQRLEKRI 214 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: 205 Number of extensions: 12 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: 396 Length of database: 225 Length adjustment: 26 Effective length of query: 370 Effective length of database: 199 Effective search space: 73630 Effective search space used: 73630 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