Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF1633 PGA1_c16550 putative branched-chain amino acid transport system, permease component
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Phaeo:GFF1633 Length = 306 Score = 144 bits (364), Expect = 2e-39 Identities = 95/309 (30%), Positives = 157/309 (50%), Gaps = 31/309 (10%) Query: 5 LQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITW 64 L+Q++NGL G + L+A G T+V+G++G+IN AHG +YM+GAF A + GS Sbjct: 7 LEQILNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGALYMVGAFAAAVVAAWTGS----- 61 Query: 65 VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124 ++ L+AS+ A G VE + R L L +++ + + + + G Sbjct: 62 ----FVLALMASLAAAAAAGALVEFLVIRKLYDRDHLDQVLATFALILIFSEGTRWVFG- 116 Query: 125 RSKPLQPILPGNLT---LMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181 S PL +P L+ + G + RL I I + + G LI RT +G RA E Sbjct: 117 -SFPLFLDVPSYLSGPISLPGGIEYPLYRLTIIAIGLVVAAGLFWLIARTRIGIQIRAGE 175 Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241 D++M LGV++ ++ +L F +GAALA +AG +V I V +G + AF V+ Sbjct: 176 SDREMIAALGVDISKLYTLVFALGAALAGLAGALVGAIQSV-QVGMGEPVLILAFVVIVI 234 Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYM----------------GSEWKDVATFTILVLVL 285 GGIGS+ GAM+G +++GL + ++ G+ + + ++ ++L Sbjct: 235 GGIGSIKGAMVGALLVGLTDTLGGVFLPQMFALFMEPASATSVGASLASMLIYILMAVIL 294 Query: 286 IFRPTGLLG 294 + RP+GL G Sbjct: 295 LVRPSGLYG 303 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: 295 Number of extensions: 22 Number of successful extensions: 5 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: 306 Length adjustment: 27 Effective length of query: 274 Effective length of database: 279 Effective search space: 76446 Effective search space used: 76446 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