Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF2762 HP15_2706 inner-membrane translocator
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Marino:GFF2762 Length = 291 Score = 177 bits (448), Expect = 3e-49 Identities = 105/298 (35%), Positives = 171/298 (57%), Gaps = 11/298 (3%) Query: 4 FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63 FLQ L G+++GA Y LIA+G+T++Y +INFA GE MIG +A ++ A+G Sbjct: 5 FLQYLFTGITIGATYALIALGFTLIYNASHVINFAQGEFLMIGG-MATVSLTAMG----- 58 Query: 64 WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQG 123 VP+ L V+L +++ + G ++R A P + + + +I IG SIF++ Q++ G Sbjct: 59 -VPMILAVVL--AVILAGILGVALQRFAIAPAKQADVVTLIIITIGASIFIRGIAQVVWG 115 Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 +Q + GAV S L + I L+ G T+T +G+A A + Sbjct: 116 KEYHVMQNFSTDQPIEVFGAVLNSQ-SLWVLGIGAILVVGLVLFFTKTLIGKAILATSMN 174 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 K+ A L+G+ V+ L F++ A L +VAG++V I + IG + G+K F AA +GG Sbjct: 175 KEAARLVGIRTQMVLMLAFMVSALLGSVAGIVVAPIT-FTSYDIGIILGLKGFVAAAIGG 233 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301 +GS GA++GG+ +G++EA +GY+ S++KD F++++LVL F P GL G +E+V Sbjct: 234 LGSGVGAVVGGLSLGIVEAMAAGYISSDYKDAVAFSMILLVLFFMPRGLFGAKVVERV 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: 315 Number of extensions: 26 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