Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BPHYT_RS32510 BPHYT_RS32510 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__BFirm:BPHYT_RS32510 Length = 286 Score = 146 bits (368), Expect = 6e-40 Identities = 93/298 (31%), Positives = 161/298 (54%), Gaps = 17/298 (5%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M +L Q++NG+ +G +Y L+A+G ++V+G++ +NFAHG Y++GA+ + A+ Sbjct: 1 MNVYLLQIVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYLLGAY---FCYQAMQWS 57 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 W L ++ ++V ++ W VE++ R + + ++ +G+++ +Q + Sbjct: 58 MSFWTALVVVPVVVGAL------AWVVEKLILRHVYAQQHEFHILVTVGLALVVQECAIL 111 Query: 121 LQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRAC 180 + G + N ++ G+ RL I T L ++ T LG A RA Sbjct: 112 IWGPLGDNVAVPDVLNGVVIWGSFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSAVRAG 171 Query: 181 EQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAV 240 + +M LLG+NV RV SL F +GAA AA+AG++ I GV D ++G A AF V Sbjct: 172 SESTEMVSLLGINVLRVFSLVFALGAATAALAGVLAAPIRGV-DPFMGIEALSVAFVVVV 230 Query: 241 LGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILV---LVLIFRPTGLLGR 295 +GG+G+ GA++GG+++G++++ M + W + A I V VL+ RP GLLGR Sbjct: 231 VGGMGNFLGALVGGLLVGIVQS----VMSTLWPEGARLMIYVAMAAVLLLRPNGLLGR 284 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: 297 Number of extensions: 21 Number of successful extensions: 7 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: 286 Length adjustment: 26 Effective length of query: 275 Effective length of database: 260 Effective search space: 71500 Effective search space used: 71500 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