Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__Phaeo:GFF774 Length = 382 Score = 111 bits (277), Expect = 3e-29 Identities = 71/232 (30%), Positives = 122/232 (52%), Gaps = 8/232 (3%) Query: 78 KMTFDNYAFVLQDTNFFDWLK----SSLIVSLGTTVIGVLVAATTGYAVSRMRFPGYRKL 133 + T +NY VL N D + ++L V++ T+I +LVAA YA++ M FPG L Sbjct: 152 EFTLENYETVLISGNSTDNMAKAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALL 211 Query: 134 MWVLLVTQMFPIAVLIVPMYQILSKLQLIDNYFGLILVYCSTAVPYCAWLLKGYFDTIPF 193 + ++ + P+ + ++P+ + +++ + Y G+ + + +P +LL+ Y IP Sbjct: 212 VAAIVGLLVVPLQLALIPLLKFHNEIGIGKGYIGVWMAHTGFGLPLAIYLLRNYMVGIPR 271 Query: 194 EIDEAGRVDGLTPFGTFFRLILPLARPGLAVAGFYSFITAFGEVAFASTFMLSDTKYTFA 253 +I E RVDG T F F R+ILPL+ P LA + F+ + ++ A F++ T T Sbjct: 272 DIIENARVDGATDFLIFVRIILPLSFPALASFAIFQFLWTWNDLLVAMVFLIDATGETTV 331 Query: 254 VGLQ--SFVSEHDAQRNLMAATA-VLVAIPVSAFFYLVQKNLVTGLTAGGTK 302 + Q + ++A +A V +A+P++ FF +QK LV GL AG K Sbjct: 332 MTKQIVELLGTRGGNWEILATSAFVSIAVPLAVFF-AMQKYLVRGLLAGSVK 382 Lambda K H 0.326 0.139 0.422 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: 339 Number of extensions: 14 Number of successful extensions: 1 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: 303 Length of database: 382 Length adjustment: 28 Effective length of query: 275 Effective length of database: 354 Effective search space: 97350 Effective search space used: 97350 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 (21.6 bits) S2: 49 (23.5 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