Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 112 bits (280), Expect = 9e-30 Identities = 65/206 (31%), Positives = 114/206 (55%), Gaps = 3/206 (1%) Query: 160 LTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPL 219 LTL +A V +V AL L +LA+ R +P + + V FI F+RG PL+ LF+ LP Sbjct: 22 LTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQLFLFYYGLPQ 81 Query: 220 FLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVI 279 L + + A++G+ L +AY+AE +R + + + Q+EAA ++G+ + M ++ Sbjct: 82 VLSVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQWEAAQSIGMTRGQMMRRIV 141 Query: 280 LPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAAL 339 LPQA ++ P +VN FI + K TSL +G+ +++ + ++ AA + E ++ A+ Sbjct: 142 LPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKEAAGS---FLYFEAFLVVAV 198 Query: 340 VFWIFCFGMSRYSMHLERKLDTGHKR 365 ++WI +S LE L+ + R Sbjct: 199 IYWILVEALSLVQRRLETHLNKAYAR 224 Lambda K H 0.330 0.144 0.469 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: 253 Number of extensions: 11 Number of successful extensions: 1 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: 365 Length of database: 224 Length adjustment: 26 Effective length of query: 339 Effective length of database: 198 Effective search space: 67122 Effective search space used: 67122 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 (21.9 bits) S2: 47 (22.7 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