Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_009565189.1 RSPH17029_RS17165 carbohydrate ABC transporter permease
Query= TCDB::O30493 (276 letters) >NCBI__GCF_000015985.1:WP_009565189.1 Length = 277 Score = 148 bits (373), Expect = 1e-40 Identities = 91/278 (32%), Positives = 142/278 (51%), Gaps = 4/278 (1%) Query: 1 MTLQQSRRLQSLLLGTLAWAIAILIFF--PIFWMVLTSFKTEIDAFATPPQFIFTPTLEN 58 M L + L+ +L L + IL+F P WM LTS E F P +F EN Sbjct: 1 MALGRKSTLRRILTVDLPMVL-ILVFTLGPYLWMALTSLTAEDKLFTRGPS-VFDLVWEN 58 Query: 59 YLHINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKML 118 Y + + +S++++ + L +SV AAYS + ++ + + LL L M Sbjct: 59 YARLFANVGFARNMLDSLIVASGTVVVGLTLSVTAAYSFSRFDFRFKRVLLLQFLLINMF 118 Query: 119 PPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDG 178 P V +++P+++L + GLLDT +ALII + I +P VWM+ +Y IPK + EAA DG Sbjct: 119 PLVLLILPLFVLMRQLGLLDTHLALIIANSTIAIPFSVWMMTSYINGIPKSLDEAAMTDG 178 Query: 179 ATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEG 238 + MVRV+LP+ G+ +T + I WNE ++L L N P+T + + Sbjct: 179 CSRLSAMVRVILPLCAPGIIATGIYIFITAWNEYLYALTLGGQNVRPITVAVQTMIGEYQ 238 Query: 239 LFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 + W L+A + P + I Q++LV GL+ GAVK Sbjct: 239 VQWGLLTAGGIVGAMPATLLFLIVQRRLVGGLTQGAVK 276 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: 214 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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 Apr 10 2024. 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