Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 135 bits (339), Expect = 2e-36 Identities = 88/276 (31%), Positives = 140/276 (50%), Gaps = 5/276 (1%) Query: 12 LMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSAALTN 71 L +SP ++L+ M++PL + + +SF LL P + G++NY +D F AL N Sbjct: 35 LYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGFENYEKLWSDRKFWIALEN 94 Query: 72 TILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPV 131 T + G+ LA+LL+ F+G+ + + LV P+ V +SAL W +F NPV Sbjct: 95 TFFWTFWSIFFQFFLGLGLAMLLNTQFFGKKLFQALVFLPWAVPTFLSALTWAWLF-NPV 153 Query: 132 NGMFAHIARGLGL--PPFDFLSQAPLASIIGIVA--WQWLPFATLILLTALQSLDREQME 187 G H LG+ P++ L LA I A W +PF + LL ALQS+ E E Sbjct: 154 IGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGELYE 213 Query: 188 AAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTASTNITY 247 AAE+DGA+ F IT+P L I + V+++TI++ I V T GGP ++ ++ Sbjct: 214 AAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTGGGPANSTQILST 273 Query: 248 LVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRM 283 ++ + D G S + +++ A+ L+ M Sbjct: 274 YIFTTAFRKLDFGYASTIAVALLIILLAYAVILLWM 309 Lambda K H 0.329 0.142 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: 276 Number of extensions: 19 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: 290 Length of database: 316 Length adjustment: 27 Effective length of query: 263 Effective length of database: 289 Effective search space: 76007 Effective search space used: 76007 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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