Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS04400 Length = 219 Score = 117 bits (294), Expect = 2e-31 Identities = 66/207 (31%), Positives = 126/207 (60%), Gaps = 12/207 (5%) Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVT---ILFFG 246 G+LLT+ AL+SM+ L LG ++AL S P + ++ Y+ + RG PL+ ++++G Sbjct: 17 GMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPLLVQIFVVYYG 76 Query: 247 QVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQ 306 + + L+ ++ L++ + AYL+E++RG + IP+GQ+ AA +LGL Q Sbjct: 77 LPGIGIALEPT------PAGVLTLSLNVGAYLSESMRGAILGIPRGQWLAAYSLGLTQGQ 130 Query: 307 TYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEV 366 R+++ PQALR+++P++ ++L++DT+L+S++ + ELL ++ ++A + + Sbjct: 131 ALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAATY---QPLPL 187 Query: 367 YLFLGVLYWLCCYGLAQLSRRLEQRLT 393 YL + +YW+ LA + R LE+RL+ Sbjct: 188 YLAVAAIYWMLSTALAHMQRLLERRLS 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: 224 Number of extensions: 9 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: 219 Length adjustment: 26 Effective length of query: 370 Effective length of database: 193 Effective search space: 71410 Effective search space used: 71410 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 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