Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate 3608246 Dshi_1650 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= BRENDA::P68183 (296 letters) >FitnessBrowser__Dino:3608246 Length = 385 Score = 90.5 bits (223), Expect = 5e-23 Identities = 68/213 (31%), Positives = 107/213 (50%), Gaps = 9/213 (4%) Query: 86 WNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFD 145 +N++ V + I + ++ AYA A M FPG+A L+ ++ + P L+L+ L L + Sbjct: 179 FNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHN 238 Query: 146 RLGEYIPFIGLNTHGGVIFAYLG-GIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFR 204 +G IG + G A+ G G+ L ++ ++ Y + + E A +DGAT +Q F Sbjct: 239 AIG-----IGKG-YLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292 Query: 205 LVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQ--QYLNPQNYLWGD 262 ++LPLS P LA I F+ ++ VA + L D T + Q + L + W Sbjct: 293 KIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEI 352 Query: 263 FAAAAVMSALPITIVFLLAQRWLVNGLTAGGVK 295 A AA +S +VF QR+LV GL AG VK Sbjct: 353 LATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 Lambda K H 0.328 0.141 0.435 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: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 296 Length of database: 385 Length adjustment: 28 Effective length of query: 268 Effective length of database: 357 Effective search space: 95676 Effective search space used: 95676 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: 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