Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate SM_b21220 SM_b21220 sugar ABC transporter permease
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Smeli:SM_b21220 Length = 293 Score = 114 bits (285), Expect = 3e-30 Identities = 87/284 (30%), Positives = 142/284 (50%), Gaps = 8/284 (2%) Query: 8 TAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMES-FTGWDNYYYFLTDPAFS 66 T A L++ P ++++ + PL T+ SF L+ G E F G NY L F Sbjct: 8 TRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLV--GTEGGFVGTANYIKMLGGSNFQ 65 Query: 67 AALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNM 126 AL T V + +V GVL ALLL+Q F G+ +R L+I P+ + V+A +W+ + Sbjct: 66 RALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLI 125 Query: 127 FMNPVNGMFAHIARGLGLPPF--DFLSQ--APLASIIGIVAWQWLPFATLILLTALQSLD 182 + NP G LGL +L + LA++I W+ P LI L ALQ++ Sbjct: 126 Y-NPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVP 184 Query: 183 REQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTAS 242 R+ A+ +DGA +RF + +P+L + V ++++TI VF I V T GGP ++ Sbjct: 185 RDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANST 244 Query: 243 TNITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGK 286 ++ LVY ++ G G++ ++ +L I+A ++ K Sbjct: 245 RTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288 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: 184 Number of extensions: 11 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: 293 Length adjustment: 26 Effective length of query: 264 Effective length of database: 267 Effective search space: 70488 Effective search space used: 70488 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 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