Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate GFF850 Psest_0864 ABC-type sugar transport systems, permease components
Query= TCDB::Q9KZ07 (334 letters) >FitnessBrowser__psRCH2:GFF850 Length = 521 Score = 131 bits (329), Expect = 4e-35 Identities = 80/240 (33%), Positives = 125/240 (52%), Gaps = 11/240 (4%) Query: 86 FVGLDNYADILWGPTAYDRFWSHFIWTIVWTAVCVGLHFFIGLGLALLLNQKL-RGRTFY 144 F G N++ +L P+ + F F WT + + V +GL LA LL +L RG+ FY Sbjct: 267 FTGFANFSRVLTEPSIREPFMQIFAWTFAFAGLTVVFTLAVGLVLASLLQWELVRGKAFY 326 Query: 145 RLILVLPWAVPTFVTVFGWRFMLADQ-GIINSALDWLHLPTPAWLEDTFWQRFSAIMVNT 203 RL+L+LP+AVP F+++ +R + G IN L+ L P W D R ++VNT Sbjct: 327 RLMLILPYAVPGFISILVFRGLFNQNFGEINLLLEGLFGIRPDWFSDPSLARTMILIVNT 386 Query: 204 WCGVPFMMVSLLGGLQSIDNSLYEASEMDGANAWQRFRYVTLPGLRSVSSTVVLLGIIWT 263 W G P+M++ +G LQ+I YEAS +DGA+ +TLP L +++ + Sbjct: 387 WLGYPYMLLLCMGLLQAIPRDQYEASAIDGASPLDNLLRITLPQLIKPLMPLLIACFAFN 446 Query: 264 FNQFAVIFLL-------FGNTAP--DAQILVTWAYQLGFGQQPRDFAQSAAYGILLLAIL 314 FN F +I LL G T P +LV++ Y++ F +DFA +AA ++ ++ Sbjct: 447 FNNFVLITLLTRGGPDIIGATTPAGTTDLLVSYTYRIAFQDSGQDFALAAAIATMIFILV 506 Lambda K H 0.328 0.142 0.468 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: 388 Number of extensions: 19 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: 334 Length of database: 521 Length adjustment: 31 Effective length of query: 303 Effective length of database: 490 Effective search space: 148470 Effective search space used: 148470 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 (21.7 bits) S2: 50 (23.9 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