Align ABC-type maltose transporter (subunit 1/3) (EC 7.5.2.1) (characterized)
to candidate HSERO_RS18950 HSERO_RS18950 glycerol-3-phosphate transporter permease
Query= BRENDA::P02916 (514 letters) >FitnessBrowser__HerbieS:HSERO_RS18950 Length = 294 Score = 110 bits (275), Expect = 7e-29 Identities = 83/278 (29%), Positives = 138/278 (49%), Gaps = 26/278 (9%) Query: 237 YQSITADGNWGDEKLSPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTV 296 YQS+ +G GY+ + NF +F D +L F T +FS + F + Sbjct: 37 YQSMLLQDAFG------GYSEFVWFDNFKTLFGDP----TYLESFRTTAIFSALVAFFGL 86 Query: 297 AVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFG 356 A+ ++LA RG ++Y+ LI PYAV + +++ L + S G ++ +LS L G Sbjct: 87 ALSLLLAVFAD-RVRRGASIYKTFLIWPYAVSPVVVGVLWMFLLSPSLGILSHVLSWL-G 144 Query: 357 VKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFK 416 + + + T A +++I W Y + + L++IP L EA+A+DGAGP + FF Sbjct: 145 LPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGLQSIPKSLIEAAAIDGAGPVKRFFT 204 Query: 417 ITLPLLIKPLTPLMIAS--FAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRI 474 I PL+ L + + +AF F+ FV++ T+GGP + T++LV Y++ Sbjct: 205 IVFPLISPTTFFLFVVNVVYAF-FDTFVIVDATTHGGPGK--------DTEILV---YKV 252 Query: 475 AFEGGGGQDFGLAAAIATLIFLLVGALAIVNLKATRMK 512 +G G D G +AA + ++ LV L +V K K Sbjct: 253 FSDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKK 290 Lambda K H 0.324 0.140 0.429 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: 362 Number of extensions: 23 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: 514 Length of database: 294 Length adjustment: 30 Effective length of query: 484 Effective length of database: 264 Effective search space: 127776 Effective search space used: 127776 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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