Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate BWI76_RS17835 BWI76_RS17835 sugar ABC transporter permease
Query= TCDB::O30493 (276 letters) >FitnessBrowser__Koxy:BWI76_RS17835 Length = 279 Score = 102 bits (255), Expect = 7e-27 Identities = 81/271 (29%), Positives = 133/271 (49%), Gaps = 20/271 (7%) Query: 19 WAIAILIFFPIFW-MVLTSFKTEI----DAFATPPQFIFTPTLENYLHINERSNYFSYAW 73 +A+ +++F FW +V T+F + A P QF F EN++ + Y Sbjct: 15 YALLLIVFVGPFWGIVATAFSGAPVKPGELLAWPNQFSF----ENFIFAWMDIGVWQYLL 70 Query: 74 NSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAKS 133 NS+L+ F T L + +S AAY++A + + L +LST MLP + +P+Y++ + Sbjct: 71 NSILVVFFGTVLQVSVSALAAYALARKKFRGVALVSLVILSTMMLPEEVIAIPLYMII-N 129 Query: 134 FGLLDTRIALIIIYTLINLPIVVW-----MVYTYFKDIPKDILEAARLDGATLWQEMVRV 188 + L +L Y + LP+V W ++ + IPK++ EAAR+DGA WQ V Sbjct: 130 WRLPFIDASLYNSYLGMILPVVGWAFSIFVLTEFMSAIPKELEEAARIDGANEWQIFFHV 189 Query: 189 LLPIAKGGLASTVLLSLILCWNEAFWSL---NLTSSNAAPLTALIASYSSPEGLFWAKLS 245 +LP+ K L + V I+ W++ L N S N P+ ++ + + E + Sbjct: 190 ILPLVKPALGTVVTFGFIMIWDQYLLPLIVVNQDSLNTIPV--ILGTLRTDESITPNIFI 247 Query: 246 AVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 A++ LA P +I QK RG+ GAVK Sbjct: 248 AITLLAMLPSIIVYLGLQKHFNRGIMSGAVK 278 Lambda K H 0.327 0.137 0.426 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: 259 Number of extensions: 15 Number of successful extensions: 3 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: 276 Length of database: 279 Length adjustment: 25 Effective length of query: 251 Effective length of database: 254 Effective search space: 63754 Effective search space used: 63754 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