Align TreT, component of Trehalose porter (characterized)
to candidate SM_b21220 SM_b21220 sugar ABC transporter permease
Query= TCDB::Q97ZC2 (275 letters) >FitnessBrowser__Smeli:SM_b21220 Length = 293 Score = 127 bits (320), Expect = 2e-34 Identities = 86/281 (30%), Positives = 150/281 (53%), Gaps = 16/281 (5%) Query: 9 FLLVLPALAYVISFAFFPTIEAVYLSFQDP-----HGGF-SLYNY-KELSYFNLSSAIIN 61 +LL+LP L + + +P ++ V LSF D GGF NY K L N A++ Sbjct: 11 WLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVT 70 Query: 62 TIVVTIGALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVFQTSG 121 T + ++A ++ LG L A +L+++F G+ AL + I+P + TVV A + ++ Sbjct: 71 TTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEY 130 Query: 122 GYANTILHSLFGLNV--NWYQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKELYYA 179 G N L L L+ +W ++L +++AD WKN P+VALI LA + ++P+++ A Sbjct: 131 GALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAA 190 Query: 180 SAIDGAGPIRRFFYITLPNLRSFIGISLILRGVQEFNIFALPLILIGEHPP----LLTTL 235 S +DGAGP RF ++ +P L + ++L+LR ++ F +F + ++ P L+ L Sbjct: 191 SLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSIL 250 Query: 236 IY-DLYTTTFPEVGLALASATILLGFIL--VFSGIVIKLSG 273 +Y + ++ G +LA LL IL ++ ++ K +G Sbjct: 251 VYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRKAAG 291 Lambda K H 0.328 0.143 0.414 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: 176 Number of extensions: 12 Number of successful extensions: 2 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: 275 Length of database: 293 Length adjustment: 26 Effective length of query: 249 Effective length of database: 267 Effective search space: 66483 Effective search space used: 66483 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: 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