Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease
Query= TCDB::O30832 (290 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 105 bits (261), Expect = 2e-27 Identities = 79/260 (30%), Positives = 131/260 (50%), Gaps = 13/260 (5%) Query: 12 LMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSAALTN 71 L ++PAVILL +++ PL + ++ F + + G SF G DN+ Y D +L N Sbjct: 15 LFMAPAVILLVVFLTYPLGLGIWLGFT--DTKIGGEGSFIGLDNFTYLAGDSLAQLSLFN 72 Query: 72 TILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPV 131 T+ V ++ + G+ LA+LL++ + R +V+ P+ V +SAL + ++ Sbjct: 73 TVFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALSALAFWWLY---- 128 Query: 132 NGMFAHIARGL---GLPP--FDFLSQAPLA--SIIGIVAWQWLPFATLILLTALQSLDRE 184 + F+ I+ L GL DFL A S + W+ +PF + LL LQ++ Sbjct: 129 DAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPS 188 Query: 185 QMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTASTN 244 EAA +DGA+ +F H+T+P LT I VV+ +F F I V T GGP A+ Sbjct: 189 LYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGGPLNATHL 248 Query: 245 ITYLVYAQSLLNYDVGGGSA 264 + L + +++ +G G+A Sbjct: 249 MATLSFQRAIPGGALGEGAA 268 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: 241 Number of extensions: 21 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: 290 Length of database: 299 Length adjustment: 26 Effective length of query: 264 Effective length of database: 273 Effective search space: 72072 Effective search space used: 72072 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