Align Maltose transport system permease protein malF aka TT_C1628, 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 Pf6N2E2_1962 Various polyols ABC transporter, permease component 1
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1962 Length = 280 Score = 124 bits (312), Expect = 2e-33 Identities = 94/280 (33%), Positives = 144/280 (51%), Gaps = 12/280 (4%) Query: 14 VLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALWNTL 73 V P++ +++L PLA Y+S + ++ EFVGLEN+AY D F NTL Sbjct: 1 VSPSVALLLLWMIVPLAMTVYFSVIRYNLLNPGENEFVGLENFAYFVTDSGFLPGALNTL 60 Query: 74 KFTVVSVSLETVLGLAIALIIH-SNFRGRGLVRTAILIPWAI-PTVVSAKMWQWMLNDVY 131 + + + G+ IA ++ S F GRG+VR ++ P+ I PTV S + + V Sbjct: 61 ILVGSVLLISVIFGVLIAALLEASEFFGRGIVRVLLISPFFIMPTVGSLIFKNLIFHPVS 120 Query: 132 GVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEELYEA 191 G++ + G +Q V +LA L SII + W+ PF LLL+ +Q + +E EA Sbjct: 121 GILAAVWKFFG--AQPVDWLAHYPLF--SIIVIVSWQWLPFAILLLMTAMQSLDQEQKEA 176 Query: 192 ASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--ATRTLA-- 247 A +DGA FW +TLP L + V ++ T+ L VF +F + P A+ LA Sbjct: 177 ARLDGAGALAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGFASTNLAYL 236 Query: 248 VYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287 +YN Q LV F D+G SA + +VI ++ +R +GK Sbjct: 237 IYN-QALVQF-DVGMASAGGLIAVVIANIAAIVLVRMIGK 274 Lambda K H 0.329 0.142 0.433 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: 203 Number of extensions: 12 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: 291 Length of database: 280 Length adjustment: 26 Effective length of query: 265 Effective length of database: 254 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