Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_008412465.1 DESHY_RS10040 carbohydrate ABC transporter permease
Query= TCDB::O30493 (276 letters) >NCBI__GCF_000315365.1:WP_008412465.1 Length = 279 Score = 192 bits (489), Expect = 5e-54 Identities = 99/272 (36%), Positives = 155/272 (56%), Gaps = 1/272 (0%) Query: 6 SRRLQSLLLGTLAWAIAIL-IFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINE 64 +R+L + +L A AIA++ PI WMVL+S KTE + F+ PP+F F PT Y + Sbjct: 8 TRKLIATVLIYTALAIAMVWALLPIIWMVLSSLKTEANMFSMPPKFTFKPTFSTYAFMFT 67 Query: 65 RSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVL 124 N+ S+ NS++ +FS+TA+ L++ Y++A +R K W++ST+M P + Sbjct: 68 EGNFGSFLKNSMIAAFSSTAIALILGTLGGYALARGNYRRGKDIAFWIISTRMTPVAAAI 127 Query: 125 MPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQE 184 +P+Y++ F L+ T L+ YT NLP +WM+ T+F ++P D+ AA +DGAT +Q Sbjct: 128 VPLYIIFAKFNLIGTTFGLVFAYTTFNLPFALWMMMTFFAELPPDMEHAAMVDGATKFQA 187 Query: 185 MVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKL 244 R+ LP GL +T +L L+ WN+ ++ TS + + + S G+ W + Sbjct: 188 FYRIALPQVTPGLVATGILCLMFAWNDFAFASVFTSHSNQTIPVAASLLVSQTGIAWGQA 247 Query: 245 SAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 A T+ P+LI G +K LVRGLS GAVK Sbjct: 248 MATGTVIITPMLIAGLAVRKYLVRGLSMGAVK 279 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: 296 Number of extensions: 2 Number of successful extensions: 1 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 24 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