Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate SMc02359 SMc02359 high-affinity branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Smeli:SMc02359 Length = 296 Score = 159 bits (401), Expect = 1e-43 Identities = 102/301 (33%), Positives = 170/301 (56%), Gaps = 16/301 (5%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M + +Q +I+ LSLG Y L+A+G ++YGI+ ++NFA+GE+ M+ + FLA GS Sbjct: 1 MAFAIQFVIDVLSLGGAYALMALGLVIIYGILRLVNFAYGELIMVAGYTM---FLASGS- 56 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 G+ W+ +A+L + +A + +G + A+RP+R+ A LI++ S LQN + Sbjct: 57 GLPWIVMAVLAVGMAIL-----FGIITDYAAFRPVRAKSVTAVLITSFAFSNLLQNAALL 111 Query: 121 LQGARSK--PLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQR 178 R + PL I +++ G L TI +IAL+ G L+ RT+LG A R Sbjct: 112 FISPRPRNVPLPDIFSQTVSI--GGAITPVRNLITIAASIALLAGVAFLMRRTTLGIAMR 169 Query: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTA 238 A + MA +LGV + +IS F + LA V G++ + G + IG + AF A Sbjct: 170 AAATNFTMARMLGVPANLIISSAFALSGFLAGVVGILWIGRIGTVVPGIGLEPLLVAFIA 229 Query: 239 AVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSE---WKDVATFTILVLVLIFRPTGLLGR 295 V+GG+ SLPGA++GG ++ LI+ + + + ++D TF++++L+L++RP GL+ Sbjct: 230 TVIGGMRSLPGAVVGGFLLALIDTTLNYTLSQDLLKFRDAFTFSLVILILLWRPDGLIRG 289 Query: 296 P 296 P Sbjct: 290 P 290 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: 305 Number of extensions: 20 Number of successful extensions: 4 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: 296 Length adjustment: 27 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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 Apr 09 2024. 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