Align Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate BPHYT_RS16105 BPHYT_RS16105 mannitol ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__BFirm:BPHYT_RS16105 Length = 291 Score = 162 bits (409), Expect = 1e-44 Identities = 84/260 (32%), Positives = 147/260 (56%), Gaps = 6/260 (2%) Query: 20 VVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQANFGRNLLNSLIVA 79 V + FP +W I++FK ++ F+P TL+ + VF ++N+ NS++++ Sbjct: 38 VALLLFFPIFWMTITAFKTEQQAYASSLFFIP---TLDSFREVFARSNYFSFAWNSILIS 94 Query: 80 GGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQTGLFNT 139 G T+L L+L V AAYA+ P V+ +LS M P + VL ++LL + +GL ++ Sbjct: 95 AGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGLLDS 154 Query: 140 HLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTGPGLVT 199 GL++ Y L LP VW+ YF +PR++ EA +DGA Q ++ +++P++ PGL + Sbjct: 155 VSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPGLAS 214 Query: 200 TGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVVTVPLV 259 T LL I +WNE +++ + S P + ++P + W + AAS++ P++ Sbjct: 215 TALLLVILSWNEAFWSINLS---SSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPIL 271 Query: 260 VLVLVFQQRIVAGLTAGAVK 279 ++ + Q+++V GLT GAVK Sbjct: 272 IVGWLSQKQLVRGLTFGAVK 291 Lambda K H 0.329 0.145 0.439 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: 161 Number of extensions: 8 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: 280 Length of database: 291 Length adjustment: 26 Effective length of query: 254 Effective length of database: 265 Effective search space: 67310 Effective search space used: 67310 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: 47 (22.7 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