Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate H281DRAFT_03746 H281DRAFT_03746 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Burk376:H281DRAFT_03746 Length = 296 Score = 120 bits (301), Expect = 4e-32 Identities = 94/285 (32%), Positives = 145/285 (50%), Gaps = 29/285 (10%) Query: 12 LMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSAALTN 71 L+I+P+++L + P+ + + L + FTG N+Y DPAF AA Sbjct: 14 LLIAPSLVLALFIISYPI-FNIVWQSLHEVSRFGAIRDFTGLQNFYTIFGDPAFLAAARR 72 Query: 72 TILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPV 131 TI+ V V+ TV+ V +AL+L+Q F+G+G+ R +V+ P+ V T++A+VW+ F N Sbjct: 73 TIVWTVFVVGGTVLISVPVALVLNQDFYGRGVARTIVMLPWSVSLTMTAVVWRWAF-NDD 131 Query: 132 NGMFAHIARGLGL----------PPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQSL 181 GM + LGL P F F P+ +GI+ +PF ILL L S+ Sbjct: 132 YGMVNVTLQRLGLIGGPIHWLATPEFAF----PVEIAVGILV--SIPFTVTILLGGLSSV 185 Query: 182 DREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTA 241 + EAA +DGASA +F +T+P L I + +L+ I++ F I V T GGP + Sbjct: 186 PGDIYEAARIDGASAWQQFRKLTLPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDNS 245 Query: 242 S-TNITYLVYAQSLLNYDVGG--GSAGGIVAVVLANIVAIFLMRM 283 + +TYL Y++G G G AV L +V +F+ M Sbjct: 246 THILVTYL--------YELGFRLGRPGEAAAVSLIMLVMLFVFSM 282 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: 208 Number of extensions: 10 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: 296 Length adjustment: 26 Effective length of query: 264 Effective length of database: 270 Effective search space: 71280 Effective search space used: 71280 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