Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 130 bits (327), Expect = 4e-35 Identities = 79/215 (36%), Positives = 129/215 (60%), Gaps = 6/215 (2%) Query: 178 LGLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGL 237 LGL PV S + LTL A+++MV +L L LLA+ R +P + L V +I FRG Sbjct: 10 LGLVPVLL---SYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGT 66 Query: 238 PLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAA 297 PL+ LF +P +L +I+ + AI+GLT+ +AY+AE++R + + + Q+EAA Sbjct: 67 PLLVQLFLFYYGLPQVLSVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQWEAA 126 Query: 298 AALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANP 357 ++G+ Q R IVLPQA RI+ P +V F+++++ T+L +G+ E++G ++ A Sbjct: 127 QSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKEAAG- 185 Query: 358 AYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 ++L Y E +L + V+YW+ L+ + RRLE L Sbjct: 186 SFL--YFEAFLVVAVIYWILVEALSLVQRRLETHL 218 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: 186 Number of extensions: 5 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: 224 Length adjustment: 26 Effective length of query: 370 Effective length of database: 198 Effective search space: 73260 Effective search space used: 73260 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