Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 132 bits (333), Expect = 4e-36 Identities = 80/216 (37%), Positives = 128/216 (59%), Gaps = 4/216 (1%) Query: 3 LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62 LD + + VP LL+ +T+ + +++L V+ L+ + R+ + V+ L +++ Sbjct: 4 LDIAYMLGLVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVL-RIPVLDQLVVLFISF 62 Query: 63 IRGTPLLVQLFILFFGLPQFGILLPAF---VCGVIGLGIYSGAYVSEVVRGAIQSIDKGQ 119 RGTPLLVQLF+ ++GLPQ +L ++GL ++ AY++E +R AI +D+ Q Sbjct: 63 FRGTPLLVQLFLFYYGLPQVLSVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQ 122 Query: 120 MEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKI 179 EAA+SIGM+ G MR +VLPQA P L N FI +IK ++L L + ++M QK Sbjct: 123 WEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKE 182 Query: 180 ISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELRL 215 + S+ E +L +AV+Y+IL A +LV RR+E L Sbjct: 183 AAGSFLYFEAFLVVAVIYWILVEALSLVQRRLETHL 218 Lambda K H 0.328 0.143 0.412 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: 135 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: 222 Length of database: 224 Length adjustment: 22 Effective length of query: 200 Effective length of database: 202 Effective search space: 40400 Effective search space used: 40400 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: 46 (22.3 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