Align Facilitated trehalose transporter Tret1-2 homolog; DmTret1-2 (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter
Query= SwissProt::Q8MKK4 (488 letters) >FitnessBrowser__Koxy:BWI76_RS21205 Length = 478 Score = 179 bits (455), Expect = 1e-49 Identities = 124/433 (28%), Positives = 208/433 (48%), Gaps = 36/433 (8%) Query: 64 FEVTKDAGS-WVGGIMPLAALAGGITGGPLIEYLGRRSTILATAVPFIVSSLLIACAVNV 122 F +T A S W + + G + G + LGR+ ++ +AV F S+ A A + Sbjct: 45 FSITDPAQSGWAMSSALVGCVFGALISGWCADKLGRKLPLILSAVLFSASAWGTAVASSF 104 Query: 123 IMILCGRFLTGFCVGIASLSLPVYLGETLQPEVRG----------TLGLLPTALGNIGIL 172 M + R + G +G+AS P+Y+ E E RG +G+L L N+ I Sbjct: 105 DMFVVYRIVGGVGIGLASALSPLYIAEVSPAEKRGRFVAVNQLTIVIGVLAAQLINLMIA 164 Query: 173 VCYVAGSF-----------MNWSMLAFLGAALPVPFLILMIIIPETPRWFVNRGQEERAR 221 G+ M W + + FL+LM +PE+PRW + G+ ERAR Sbjct: 165 EPVATGATQQMIVETWNGQMGWRWMFGAELVPALAFLVLMFFVPESPRWLMKAGKPERAR 224 Query: 222 KALKWLRGKEADVEPELKELMQSQADADRQATQNTCLELFKRNNLKPLSI-SLGLMFFQQ 280 AL+ + G + L+++ + + + + L +KP+ I + L FQQ Sbjct: 225 AALERI-GSADYADRILRDIAHTLEKDNHKVSYGALLA----PQVKPIVIIGMVLAVFQQ 279 Query: 281 FSGINAVIFYTVQIFKDAGSTIDSNLSTIIV-GVVNFFATFMGIILIDRLGRKILLYVSD 339 + GIN + Y +IF AG I+S L +I+ GVVN T + L+D++GR+ L+ + Sbjct: 280 WCGINVIFNYAQEIFASAGFDINSTLKSIVATGVVNLVFTLAALPLVDKIGRRKLMLLGA 339 Query: 340 IAMIVTLSILGGFFYCKAHGPDVSHLGWLPLTCFVIYILGFSLGFGPIPWLMMGEILPAK 399 + + ++ G + + +GW L + I ++L P+ W+++ EI P + Sbjct: 340 SGLTLIYVLIAGAYA-------MGIMGWPVLLLVLAAIAIYALTLAPVTWVLLAEIFPNR 392 Query: 400 IRGPAASVVTAFNWFCTFVVTKTFQDLTVAMGAHGAFWLFGAICIVGLFFVIIFVPETRG 459 +RG A S+ T W F++T TF L +GA G+F L+G IC G +++ VPET+G Sbjct: 393 VRGLAMSLGTLALWIACFLLTYTFPLLNAGLGAAGSFLLYGVICAAGYLYILRNVPETKG 452 Query: 460 KSLEEIERKMMGR 472 +LE +E ++ R Sbjct: 453 VTLEALEEQLAQR 465 Lambda K H 0.328 0.142 0.436 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: 595 Number of extensions: 34 Number of successful extensions: 6 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: 488 Length of database: 478 Length adjustment: 34 Effective length of query: 454 Effective length of database: 444 Effective search space: 201576 Effective search space used: 201576 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: 52 (24.6 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