Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF247 PGA1_c02590 putative high-affinity branched-chain amino acid transport system permease protein LivH
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Phaeo:GFF247 Length = 291 Score = 167 bits (424), Expect = 2e-46 Identities = 101/298 (33%), Positives = 165/298 (55%), Gaps = 11/298 (3%) Query: 5 LQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITW 64 +Q L++GL+ G +YGLIA+G+ ++Y +NFA G+ M+GAFV L G + Sbjct: 4 VQLLVSGLANGCVYGLIALGFVLIYKATEAVNFAQGDFMMLGAFVTL------GLTNAEY 57 Query: 65 VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124 + L + S+ A G+ ++ + R L + A +I I + ++ + + G Sbjct: 58 LHLPFWLAAPLSIAIMAGLGYLLDLVILRHLFGQNQTAVVILTIALGFVIRFFAGAIWGH 117 Query: 125 RSKPLQ-PILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 + L+ P+ G++ L V + LA I++T+ L + Q RT LG A +A Q+ Sbjct: 118 EPQTLESPLALGDVQL--AGVVLGLADLAIIIVTVLLTWSLYQFFQRTKLGLAMQAASQN 175 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 + A +G+ V RV L + + A AAVAG++ G ID G L G+KAF AAV+GG Sbjct: 176 QMAAYFMGIPVKRVQGLIWGLSGATAAVAGIL-FASKGAIDPNAGLL-GIKAFAAAVIGG 233 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301 GSLPGA+ GG+++G+IE F + Y+ + + +A + +L+ VL+FRP GL + +KV Sbjct: 234 FGSLPGALAGGLIVGVIEPFAARYLAAGYSQIAPYVLLLAVLVFRPHGLFSQVRTKKV 291 Lambda K H 0.329 0.144 0.425 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: 307 Number of extensions: 15 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: 301 Length of database: 291 Length adjustment: 26 Effective length of query: 275 Effective length of database: 265 Effective search space: 72875 Effective search space used: 72875 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